Substrate Specificity
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Amino Acid Sequence
Sensitivity and Specificity
Binding Sites
Models, Molecular
Catalysis
Sequence Homology, Amino Acid
Catalytic Domain
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Base Sequence
Crystallography, X-Ray
Mutagenesis, Site-Directed
Hydrogen-Ion Concentration
Cloning, Molecular
Protein Binding
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Structure-Activity Relationship
Mutation
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Antibody Specificity
Isoenzymes
Electrophoresis, Polyacrylamide Gel
Molecular Structure
Amino Acids
Peptides
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Enzyme Stability
Phosphorylation
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Stereoisomerism
Temperature
Recombinant Fusion Proteins
Endopeptidases
Serine Endopeptidases
Chromatography, High Pressure Liquid
Alcohol Oxidoreductases
A subclass of enzymes which includes all dehydrogenases acting on primary and secondary alcohols as well as hemiacetals. They are further classified according to the acceptor which can be NAD+ or NADP+ (subclass 1.1.1), cytochrome (1.1.2), oxygen (1.1.3), quinone (1.1.5), or another acceptor (1.1.99).
Protein Structure, Secondary
Carbohydrate Sequence
Saccharomyces cerevisiae
Cattle
Protein Engineering
Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.
Enzyme Activation
Oxidation-Reduction
A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).
Models, Chemical
Acyltransferases
Chromatography, Gel
Amino Acid Motifs
DNA, Complementary
Peptide Library
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Oligosaccharides
Liver
Biological Transport
Oxidoreductases
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
Hydrolases
Any member of the class of enzymes that catalyze the cleavage of the substrate and the addition of water to the resulting molecules, e.g., ESTERASES, glycosidases (GLYCOSIDE HYDROLASES), lipases, NUCLEOTIDASES, peptidases (PEPTIDE HYDROLASES), and phosphatases (PHOSPHORIC MONOESTER HYDROLASES). EC 3.
Carrier Proteins
Adenosine Triphosphate
Plasmids
Acyl Coenzyme A
Biocatalysis
Membrane Transport Proteins
Peptide Hydrolases
Protein Kinases
Conserved Sequence
Aminopeptidases
beta-Glucosidase
Pseudomonas
Mixed Function Oxygenases
Widely distributed enzymes that carry out oxidation-reduction reactions in which one atom of the oxygen molecule is incorporated into the organic substrate; the other oxygen atom is reduced and combined with hydrogen ions to form water. They are also known as monooxygenases or hydroxylases. These reactions require two substrates as reductants for each of the two oxygen atoms. There are different classes of monooxygenases depending on the type of hydrogen-providing cosubstrate (COENZYMES) required in the mixed-function oxidation.
Carboxylic Ester Hydrolases
Mutagenesis
Peptide Fragments
Enzyme Inhibitors
Dioxygenases
Cations, Divalent
Cysteine Endopeptidases
Membrane Proteins
Protease Inhibitors
Rabbits
Binding, Competitive
Models, Biological
Saccharomyces cerevisiae Proteins
Alanine
Mass Spectrometry
Streptomyces
Peptide Synthases
Organ Specificity
Chromatography
Techniques used to separate mixtures of substances based on differences in the relative affinities of the substances for mobile and stationary phases. A mobile phase (fluid or gas) passes through a column containing a stationary phase of porous solid or liquid coated on a solid support. Usage is both analytical for small amounts and preparative for bulk amounts.
Phosphoric Monoester Hydrolases
Cell Membrane
Metals
Chromatography, Ion Exchange
Dimerization
NAD
A coenzyme composed of ribosylnicotinamide 5'-diphosphate coupled to adenosine 5'-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). (Dorland, 27th ed)
Magnetic Resonance Spectroscopy
Sulfotransferases
Transfection
Cytochrome P-450 Enzyme System
A superfamily of hundreds of closely related HEMEPROTEINS found throughout the phylogenetic spectrum, from animals, plants, fungi, to bacteria. They include numerous complex monooxygenases (MIXED FUNCTION OXYGENASES). In animals, these P-450 enzymes serve two major functions: (1) biosynthesis of steroids, fatty acids, and bile acids; (2) metabolism of endogenous and a wide variety of exogenous substrates, such as toxins and drugs (BIOTRANSFORMATION). They are classified, according to their sequence similarities rather than functions, into CYP gene families (>40% homology) and subfamilies (>59% homology). For example, enzymes from the CYP1, CYP2, and CYP3 gene families are responsible for most drug metabolism.
Chromatography, Affinity
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Bacillus
Pichia
Structural Homology, Protein
Aspartic Acid
Protein Processing, Post-Translational
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
Serine
Adenosine Triphosphatases
Coumarins
Chromatography, Thin Layer
Oxygenases
HeLa Cells
Factor Xa
Glutathione Transferase
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Pseudomonas putida
Sequence Analysis, DNA
Enzyme Assays
Methods used to measure the relative activity of a specific enzyme or its concentration in solution. Typically an enzyme substrate is added to a buffer solution containing enzyme and the rate of conversion of substrate to product is measured under controlled conditions. Many classical enzymatic assay methods involve the use of synthetic colorimetric substrates and measuring the reaction rates using a spectrophotometer.
N-Acetylgalactosaminyltransferases
Manganese
A trace element with atomic symbol Mn, atomic number 25, and atomic weight 54.94. It is concentrated in cell mitochondria, mostly in the pituitary gland, liver, pancreas, kidney, and bone, influences the synthesis of mucopolysaccharides, stimulates hepatic synthesis of cholesterol and fatty acids, and is a cofactor in many enzymes, including arginase and alkaline phosphatase in the liver. (From AMA Drug Evaluations Annual 1992, p2035)
Methyltransferases
Protein Structure, Quaternary
Hydroxylation
Swine
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
Ligands
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Erythrocyte Membrane
Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
L Cells (Cell Line)
Tyrosine
COS Cells
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Chromatography, DEAE-Cellulose
Crystallization
Directed Molecular Evolution
The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
Acetyltransferases
NADP
Nicotinamide adenine dinucleotide phosphate. A coenzyme composed of ribosylnicotinamide 5'-phosphate (NMN) coupled by pyrophosphate linkage to the 5'-phosphate adenosine 2',5'-bisphosphate. It serves as an electron carrier in a number of reactions, being alternately oxidized (NADP+) and reduced (NADPH). (Dorland, 27th ed)
Cytosol
Nucleic Acid Conformation
Plant Proteins
Transaminases
Isoelectric Point
Glycine
Thermodynamics
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
alpha-Mannosidase
An enzyme that catalyzes the HYDROLYSIS of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides. The enzyme plays a role in the processing of newly formed N-glycans and in degradation of mature GLYCOPROTEINS. There are multiple isoforms of alpha-mannosidase, each having its own specific cellular location and pH optimum. Defects in the lysosomal form of the enzyme results in a buildup of mannoside intermediate metabolites and the disease ALPHA-MANNOSIDOSIS.
Hydrogen Bonding
Tellurium
Alcohols
N-Glycosyl Hydrolases
Gene Expression
Evolution, Molecular
Lipase
Microsomes, Liver
Phenylalanine
Signal Transduction
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Blotting, Western
Enzymes
Spectrophotometry
Potassium Magnesium Aspartate
Oligodeoxyribonucleotides
Penicillin Amidase
RNA, Messenger
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Threonine
Macromolecular Substances
Methylation
Nucleotides
Prodigious substrate specificity of AAC(6')-APH(2"), an aminoglycoside antibiotic resistance determinant in enterococci and staphylococci. (1/34326)
BACKGROUND: High-level gentamicin resistance in enterococci and staphylococci is conferred by AAC(6')-APH(2"), an enzyme with 6'-N-acetyltransferase and 2"-O-phosphotransferase activities. The presence of this enzyme in pathogenic gram-positive bacteria prevents the successful use of gentamicin C and most other aminoglycosides as therapeutic agents. RESULTS: In an effort to understand the mechanism of aminoglycoside modification, we expressed AAC(6')-APH(2") in Bacillus subtilis. The purified enzyme is monomeric with a molecular mass of 57 kDa and displays both the expected aminoglycoside N-acetyltransferase and O-phosphotransferase activities. Structure-function analysis with various aminoglycosides substrates reveals an enzyme with broad specificity in both enzymatic activities, accounting for AAC(6')-APH(2")'s dramatic negative impact on clinical aminoglycoside therapy. Both lividomycin A and paromomycin, aminoglycosides lacking a 6'-amino group, were acetylated by AAC(6')-APH(2"). The infrared spectrum of the product of paromomycin acetylation yielded a signal consistent with O-acetylation. Mass spectral and nuclear magnetic resonance analysis of the products of neomycin phosphorylation indicated that phosphoryl transfer occurred primarily at the 3'-OH of the 6-aminohexose ring A, and that some diphosphorylated material was also present with phosphates at the 3'-OH and the 3"'-OH of ring D, both unprecedented observations for this enzyme. Furthermore, the phosphorylation site of lividomycin A was determined to be the 5"-OH of the pentose ring C. CONCLUSIONS: The bifunctional AAC(6')-APH(2") has the capacity to inactivate virtually all clinically important aminoglycosides through N- and O-acetylation and phosphorylation of hydroxyl groups. The extremely broad substrate specificity of this enzyme will impact on future development of aminoglycosides and presents a significant challenge for antibiotic design. (+info)Mechanism and specificity of the terminal thioesterase domain from the erythromycin polyketide synthase. (2/34326)
BACKGROUND: Polyketides are important compounds with antibiotic and anticancer activities. Several modular polyketide synthases (PKSs) contain a terminal thioesterase (TE) domain probably responsible for the release and concomitant cyclization of the fully processed polyketide chain. Because the TE domain influences qualitative aspects of product formation by engineered PKSs, its mechanism and specificity are of considerable interest. RESULTS: The TE domain of the 6-deoxyerythronolide B synthase was overexpressed in Escherichia coli. When tested against a set of N-acetyl cysteamine thioesters the TE domain did not act as a cyclase, but showed significant hydrolytic specificity towards substrates that mimic important features of its natural substrate. Also the overall rate of polyketide chain release was strongly enhanced by a covalent connection between the TE domain and the terminal PKS module (by as much as 100-fold compared with separate TE and PKS 'domains'). CONCLUSIONS: The inability of the TE domain alone to catalyze cyclization suggests that macrocycle formation results from the combined action of the TE domain and a PKS module. The chain-length and stereochemical preferences of the TE domain might be relevant in the design and engineered biosynthesis of certain novel polyketides. Our results also suggest that the TE domain might loop back to catalyze the release of polyketide chains from both terminal and pre-terminal modules, which may explain the ability of certain naturally occurring PKSs, such as the picromycin synthase, to generate both 12-membered and 14-membered macrolide antibiotics. (+info)A genetic model of substrate deprivation therapy for a glycosphingolipid storage disorder. (3/34326)
Inherited defects in the degradation of glycosphingolipids (GSLs) cause a group of severe diseases known as GSL storage disorders. There are currently no effective treatments for the majority of these disorders. We have explored a new treatment paradigm, substrate deprivation therapy, by constructing a genetic model in mice. Sandhoff's disease mice, which abnormally accumulate GSLs, were bred with mice that were blocked in their synthesis of GSLs. The mice with simultaneous defects in GSL synthesis and degradation no longer accumulated GSLs, had improved neurologic function, and had a much longer life span. However, these mice eventually developed a late-onset neurologic disease because of accumulation of another class of substrate, oligosaccharides. The results support the validity of the substrate deprivation therapy and also highlight some limitations. (+info)Activation of Src in human breast tumor cell lines: elevated levels of phosphotyrosine phosphatase activity that preferentially recognizes the Src carboxy terminal negative regulatory tyrosine 530. (4/34326)
Elevated levels of Src kinase activity have been reported in a number of human cancers, including colon and breast cancer. We have analysed four human breast tumor cell lines that exhibit high levels of Src kinase activity, and have determined that these cell lines also exhibit a high level of a phosphotyrosine phosphatase activity that recognizes the Src carboxy-terminal P-Tyr530 negative regulatory site. Total Src kinase activity in these cell lines is elevated as much as 30-fold over activity in normal control cells and specific activity is elevated as much as 5.6-fold. When the breast tumor cells were grown in the presence of the tyrosine phosphatase inhibitor vanadate, Src kinase activity was reduced in all four breast tumor cell lines, suggesting that Src was being activated by a phosphatase which could recognize the Tyr530 negative regulatory site. In fractionated cell extracts from the breast tumor cells, we found elevated levels of a membrane associated tyrosine phosphatase activity that preferentially dephosphorylated a Src family carboxy-terminal phosphopeptide containing the regulatory tyrosine 530 site. Src was hypophosphorylated in vivo at tyrosine 530 in at least two of the tumor cell lines, further suggesting that Src was being activated by a phosphatase in these cells. In preliminary immunoprecipitation and antibody depletion experiments, we were unable to correlate the major portion of this phosphatase activity with several known phosphatases. (+info)Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. (5/34326)
The lysosomal cysteine proteases cathepsins S and L play crucial roles in the degradation of the invariant chain during maturation of MHC class II molecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifically inhibits cathepsin L but not S. The crystal structure of the p41 fragment, a homologue of the thyroglobulin type-1 domains, has been determined at 2.0 A resolution in complex with cathepsin L. The structure of the p41 fragment demonstrates a novel fold, consisting of two subdomains, each stabilized by disulfide bridges. The first subdomain is an alpha-helix-beta-strand arrangement, whereas the second subdomain has a predominantly beta-strand arrangement. The wedge shape and three-loop arrangement of the p41 fragment bound to the active site cleft of cathepsin L are reminiscent of the inhibitory edge of cystatins, thus demonstrating the first example of convergent evolution observed in cysteine protease inhibitors. However, the different fold of the p41 fragment results in additional contacts with the top of the R-domain of the enzymes, which defines the specificity-determining S2 and S1' substrate-binding sites. This enables inhibitors based on the thyroglobulin type-1 domain fold, in contrast to the rather non-selective cystatins, to exhibit specificity for their target enzymes. (+info)Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. (6/34326)
We report striking differences in the substrate specificities of two human SR proteins, SF2/ASF and SC35, in constitutive splicing. beta-Globin pre-mRNA (exons 1 and 2) is spliced indiscriminately with either SR protein. Human immunodeficiency virus tat pre-mRNA (exons 2 and 3) and immunoglobulin mu-chain (IgM) pre-mRNA (exons C3 and C4) are preferentially spliced with SF2/ASF and SC35, respectively. Using in vitro splicing with mutated or chimeric derivatives of the tat and IgM pre-mRNAs, we defined specific combinations of segments in the downstream exons, which mediate either positive or negative effects to confer SR protein specificity. A series of recombinant chimeric proteins consisting of domains of SF2/ASF and SC35 in various combinations was used to localize trans-acting domains responsible for substrate specificity. The RS domains of SF2/ASF and SC35 can be exchanged without effect on substrate specificity. The RNA recognition motifs (RRMs) of SF2/ASF are active only in the context of a two-RRM structure, and RRM2 has a dominant role in substrate specificity. In contrast, the single RRM of SC35 can function alone, but its substrate specificity can be influenced by the presence of an additional RRM. The RRMs behave as modules that, when present in different combinations, can have positive, neutral, or negative effects on splicing, depending upon the specific substrate. We conclude that SR protein-specific recognition of specific positive and negative pre-mRNA exonic elements via one or more RRMs is a crucial determinant of the substrate specificity of SR proteins in constitutive splicing. (+info)Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. (7/34326)
Pseudouridine (Psi) residues were localized in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (UsnRNAs) by using the chemical mapping method. In contrast to vertebrate UsnRNAs, S. cerevisiae UsnRNAs contain only a few Psi residues, which are located in segments involved in intermolecular RNA-RNA or RNA-protein interactions. At these positions, UsnRNAs are universally modified. When yeast mutants disrupted for one of the several pseudouridine synthase genes (PUS1, PUS2, PUS3, and PUS4) or depleted in rRNA-pseudouridine synthase Cbf5p were tested for UsnRNA Psi content, only the loss of the Pus1p activity was found to affect Psi formation in spliceosomal UsnRNAs. Indeed, Psi44 formation in U2 snRNA was abolished. By using purified Pus1p enzyme and in vitro-produced U2 snRNA, Pus1p is shown here to catalyze Psi44 formation in the S. cerevisiae U2 snRNA. Thus, Pus1p is the first UsnRNA pseudouridine synthase characterized so far which exhibits a dual substrate specificity, acting on both tRNAs and U2 snRNA. As depletion of rRNA-pseudouridine synthase Cbf5p had no effect on UsnRNA Psi content, formation of Psi residues in S. cerevisiae UsnRNAs is not dependent on the Cbf5p-snoRNA guided mechanism. (+info)The human F box protein beta-Trcp associates with the Cul1/Skp1 complex and regulates the stability of beta-catenin. (8/34326)
Ubiquitin-conjugation targets numerous cellular regulators for proteasome-mediated degradation. Thus, the identification of ubiquitin ligases and their physiological substrates is crucially important, especially for those cases in which aberrant levels of regulatory proteins (e.g., beta-catenin, p27) result from a deregulated ubiquitination pathway. In yeast, the proteolysis of several G1 regulators is controlled by ubiquitin ligases (or SCFs) formed by three subunits: Skp1, Cul A (Cdc53), and one of many F-box proteins. Specific F-box proteins (Fbps) recruit different substrates to the SCF. Although many Fbps have been identified in mammals, their specific substrates and the existence of multiple SCFs have not yet been reported. We have found that one human Fbp, beta-Trcp (beta-Transducin repeat containing protein), does indeed form a novel SCF with human Skp1 and Cul1. Consistent with recent reports indicating that Xenopus and Drosophila beta-Trcp homologs act as negative regulators of the Wnt/beta-catenin signaling pathway, we report here that human beta-Trcp interacts with beta-catenin in vivo. Furthermore, beta-catenin is specifically stabilized in vivo by the expression of a dominant negative beta-Trcp. These results indicate that the Cul1/Skp1/beta-Trcp complex forms a ubiquitin ligase that mediates the degradation of beta-catenin. (+info)
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UGE3 protein (Arabidopsis thaliana) - STRING network view
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1h27 - Proteopedia, life in 3D
Structural Basis of Caspase-3 Substrate Specificity Revealed by Crysta by Bin Fang
Identification of Crucial Amino Acids in Mouse Aldehyde Oxidase 3 That Determine Substrate Specificity - pdf descargar
Cell Biology group | Department of Biophysics and Cell Biology
Substrate specificity of hyaluronidases tested on polya | Open-i
Diethyl 4-Methylbenzylphosphonate - DrugBank
Designing of Substrates and Inhibitors of Bovine α-Chymotryp...: Ingenta Connect
Defining Substrate Specificities for Lipase and Phospholipase Candidates | Protocol
To boost our understanding of Taspase1s substrate specificity we used our biosensor assay mixed with positional scanning...
Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials : Bioinformatics - oi
ETS-targeted therapy: can it substitute for MEK inhibitors? | Clinical and Translational Medicine | Full Text
Lirias: pKa modulation of the acid/base catalyst within GH32 and GH68: a role in substrate/inhibitor specificity?
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Energetics & Enzymes
Patent US8084685 - Apparatus for making controlled segregated phase domain structures - Google Patents
Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs | Science Signaling
ProteomeXchange Dataset PXD014199
Evaluation of atypical cytochrome P450 kinetics with two-substrate models: evidence that multiple substrates can simultaneously...
AID 1078669 - Inhibition of human P70S6K catalytic domain expressed in baculovirus assessed as substrate phosphorylation using...
AID 1078796 - Inhibition of human FER catalytic domain expressed in baculovirus assessed as substrate phosphorylation using...
Src Optimal Peptide Substrate | Peptide | MCE
Identification of Protein Kinase Substrates by the Kinase‐Interacting Substrate Screening (KISS) Approach - Current Protocols
RCSB PDB
for 1UN4
The Effect Of Substrate On The Rate Of Respiration On Yeast Essay
Research Interests
Histone acetyltransferase
Substrate binding and specificity[edit]. The structures of several HAT domains bound to acetyl-CoA and histone substrate ... 4 Substrate binding and specificity *4.1 Lysine selectivity *4.1.1 GNAT family ... The formation of multisubunit complexes has been observed to modulate the substrate specificity of HATs.[10] In general, while ... For example, the lysine specificity of MYST family HATs toward their histone substrates becomes more restricted when they ...
ACP1
Implications for substrate specificity". J. Biol. Chem. 273 (34): 21714-20. doi:10.1074/jbc.273.34.21714. PMID 9705307.. ...
Lewis C. Cantley
Use of Oriented Peptide Libraries to determine phosphopeptide binding specificity and protein kinase substrate specificity[edit ... 2.2 Use of Oriented Peptide Libraries to determine phosphopeptide binding specificity and protein kinase substrate specificity ... This approach was used to characterize the substrate specificity of a large number of protein kinases. The kinase specificity ... P as a substrate, in fact required PtdIns(5)P as a substrate to produce PtdIns(4,5)P2.[34] Further research demonstrated that ...
Isopenicillin N synthase
Retrieved from Encyclopædia Britannica Online: [1] Miller FD, Chapman JL, Queener SW (1992). "Substrate specificity of ... This allows for the binding of the substrate ACV to the deprotonated thiol group of the cysteine residue. This ligation of the ... and two water molecules in the absence of a bound substrate. Just two histidine residues and one aspartic acid residue are ... "Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation". Nature. 387 (6635): ...
Tryptophan 7-halogenase
These enzymes halogenate without substrate specificity and regioselectivity. The first tryptophan 7-halogenase was isolated in ... These results suggest that for larger substrates, perhaps the entirety of the substrate molecule is not enclosed in the active ... Enzyme activity was evolved with a known substrate that bears structural similarity to the target substrate, then variants with ... Site-directed mutagenesis has also been employed for expanding substrate scope. Tryptophan substrate interacts with numerous ...
Xylose isomerase
It is now known that isomerases have broad substrate specificity. Most pentoses and some hexoses are all substrates for D- ... Metal site 1 binds the substrate tightly, while metal site two binds the substrate loosely. Both share an acid residue Glutamic ... The first metal, mentioned earlier, coordinates to O3 and O4, and is used to dock the substrate. In the isomerization of xylose ... state consists of a high energy carbonium ion that is stabilized through all the metal interactions with the sugar substrate. ...
17β-Hydroxysteroid dehydrogenase
Substrate specificities. Preferred cofactor. Catalytic preference. Tissue distribution. Expression profile. Pathology 1. ... HSD17B10: Also known as 2-methyl-3-hydroxybutyryl-CoA dehydrogenase (MHBD). Substrates include steroids, neurosteroids, fatty ...
Flavin-containing monooxygenase 3
A second precaution with respect to predicting FMO enzyme substrate specificity is that factors other than size and charge must ... substrate specificity and role in drug metabolism". Curr. Drug Metab. 1 (2): 181-191. doi:10.2174/1389200003339135. PMID ... This enzyme has a wide substrate specificity, including the dietary-derived tertiary amines trimethylamine, tyramine and ... Other drug substrates have been used for both in vitro and in vivo analyses. ... FMO3 is the most abundantly expressed FMO in ...
MAP2K6
... comparison of its substrate specificity with that of other SAP kinases". The EMBO Journal. 16 (12): 3563-71. doi:10.1093/emboj/ ... Dual specificity mitogen-activated protein kinase kinase 6 also known as MAP kinase kinase 6 (MAPKK 6) or MAPK/ERK kinase 6 is ... MAPKK 6 is a member of the dual specificity protein kinase family, which functions as a mitogen-activated protein (MAP) kinase ... "Nuclear export of the stress-activated protein kinase p38 mediated by its substrate MAPKAP kinase-2". Current Biology. 8 (19): ...
Walker motifs
Implications for substrate specificity". J. Biol. Chem. 273 (34): 21714-20. doi:10.1074/jbc.273.34.21714. PMID 9705307. ... and is also found in a variety of proteins with phosphorylated substrates. These include ATP synthase (α and β subunits), ...
PNGase F
Multiplicity and substrate specificity". Biochimica et Biophysica Acta (BBA) - Enzymology. 657 (2): 457-67. doi:10.1016/0005- ... Tachibana Y, Yamashita K, Kobata A (1982). "Substrate specificity of mammalian endo-beta-N-acetylglucosaminidase: study with ... PNGase F lacks selectivity for outer carbohydrate structure, resulting in broad specificity, making it a useful tool for ... These endoglycosidases have more specificity in cleavage and are less sensitive to protein conformation than PNGase F. All of ...
Adenosine kinase
Substrate and inhibitor specificity". The Journal of Biological Chemistry. 254 (7): 2346-52. PMID 218934. Cass CE, Selner M, ... Compounds that are substrates for AdK include the N-nucleosides toyocamycin, tubercidin and 6-methylmecaptopurine riboside; the ... identification of a novel motif implicated in phosphate and magnesium ion binding and substrate inhibition". Biochemistry. 41 ( ...
DDT-dehydrochlorinase
Substrate and cofactor specificity". J. Biol. Chem. 234 (8): 2129-32. PMID 13673025. Moorefield HH (1956). "Purification of DDT ... this enzyme has one substrate, 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane, and two products, 1,1-dichloro-2,2-bis(4- ...
Amphiphysin
"Dynamin is a minibrain kinase/dual specificity Yak1-related kinase 1A substrate". The Journal of Biological Chemistry. 277 (20 ... "Specificity of the binding of synapsin I to Src homology 3 domains". The Journal of Biological Chemistry. 275 (38): 29857-67. ... bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity". The ...
Enzyme promiscuity
Villiers BR, Hollfelder F (March 2009). "Mapping the limits of substrate specificity of the adenylation domain of TycA". ... whereas the ability to act upon different substrates is called substrate promiscuity or substrate ambiguity. The term latent ... Enzymes are evolved to catalyse a particular reaction on a particular substrate with a high catalytic efficiency (kcat/KM, cf. ... When the specificity of enzyme was probed, it was found that it was highly selective against natural amino acids that were not ...
Ribonucleotide reductase
In addition to controlling activity, the allosteric mechanism also regulates the substrate specificity and ensures the enzyme ... RNR1 contains both allosteric sites, mediating regulation of substrate specificity and activity. Depending on the allosteric ... Reduction of NDP substrates occurs under aerobic conditions. Class I reductases are divided into IA and IB due to differences ... The substrates for RNR are ADP, GDP, CDP and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme ( ...
Protease
Specificity[edit]. Proteolysis can be highly promiscuous such that a wide range of protein substrates are hydrolysed. This is ... Promiscuous proteases typically bind to a single amino acid on the substrate and so only have specificity for that residue. For ... TopFIND - database of protease specificity, substrates, products and inhibitors. *MEROPS - Database of protease evolutionary ... have high specificity and only cleave very restricted set of substrate sequences. They are therefore a common target for ...
Violaxanthin de-epoxidase
Lipid composition and substrate specificity". Archives of Biochemistry and Biophysics. 190 (2): 514-22. doi:10.1016/0003-9861( ... Goss R (September 2003). "Substrate specificity of the violaxanthin de-epoxidase of the primitive green alga Mantoniella ...
Strictosidine synthase
... the enzyme possesses a high degree of substrate specificity, with the indole moiety of tryptamine required for substrate ... McCoy E, Galan MC, O'Connor SE (2006). "Substrate specificity of strictosidine synthase". Bioorg. Med. Chem. Lett. 16 (9): 2475 ... have suggested that strictosidine synthase can be easily manipulated to have a broader range of substrate specificity. For ... Upon substrate binding, secologanin's position is located at the pocket's entrance, where the positively charged residues His ...
EPHX1
... has broad substrate specificity. EPHX1 detoxifies low molecular weight chemicals, e.g., butadiene, benzene, styrene, etc ... Oesch F (1974). "Purification and specificity of a human microsomal epoxide hydratase". Biochem. J. 139 (1): 77-88. doi:10.1042 ... Androstene oxide and epoxyestratrienol have been shown as endogenous EPHX1 substrates. EPHX1 also metabolizes endocannabinoid 2 ... Structure-activity relationships for substrates and inhibitors". Biochemistry. 10 (26): 4858-66. doi:10.1021/bi00802a005. PMID ...
Tryptophan alpha,beta-oxidase
Substrate specificity and mechanistic implications". J. Biol. Chem. 270 (40): 23540-5. doi:10.1074/jbc.270.40.23540. PMID ... the two substrates of this enzyme are L-tryptophan and O2, whereas its two products are alpha,beta-didehydrotryptophan and H2O2 ...
ALPPL2
Implication for a substrate specificity". The Journal of Biological Chemistry. 276 (12): 9158-65. doi:10.1074/jbc.M009250200. ...
Trypanothione-disulfide reductase
Marsh IR, Bradley M (1997). "Substrate specificity of trypanothione reductase". Eur. J. Biochem. 243 (3): 690-4. doi:10.1111/j. ... the two substrates of this enzyme are trypanothione and NADP+, whereas its 3 products are trypanothione disulfide, NADPH, and ... Subversive Substrates and Antitrypanosomal Properties". ChemMedChem. 2 (12): 1708-12. doi:10.1002/cmdc.200700172. PMID 17918760 ...
Alberto Sols
Sols, Alberto; Crane, Robert (1954). "Substrate specificity of brain hexokinase". Journal of Biological Chemistry. 210 (2): 581 ... "The Kinetics of Yeast Hexokinase in the Light of the Induced Fit Involved in the Binding of its Sugar Substrate". European ...
Robert K. Crane
"Substrate specificity of brain hexokinase". Journal of Biological Chemistry 210, 1954, pp. 581-595. Robert K. Crane, Richard A ...
Fructose-bisphosphate aldolase)-lysine N-methyltransferase
"Polypeptide substrate specificity of PsLSMT. A set domain protein methyltransferase". The Journal of Biological Chemistry. 282 ...
Polyphenol oxidase
McLarin, Mark-Anthony; Leung, Ivanhoe K. H. (2020). "Substrate Specificity of Polyphenol Oxidase". Crit. Rev. Biochem. Mol. ... Because the substrates of these PPO reactions are located in the vacuoles of plant cells damaged mainly by improper harvesting ... PPO may accept monophenols and/or o-diphenols as substrates. The enzyme works by catalyzing the o-hydroxylation of monophenol ... The two isoenzymes prefer different substrates, as jr PPO1 shows a higher activity towards monophenols, whereas jr PPO2 is more ...
Placental alkaline phosphatase
Implication for a substrate specificity". J. Biol. Chem. 276 (12): 9158-65. doi:10.1074/jbc.M009250200. PMID 11124260. Spurway ... substrate proteins associate with the transamidase subunit gpi8p". J. Biol. Chem. 276 (19): 15975-82. doi:10.1074/jbc. ...
ADH7
Structural basis for substrate specificity". The Journal of Biological Chemistry. 272 (30): 18558-63. doi:10.1074/jbc.272.30. ... Active-site amino acid sequence explains substrate specificity compared with liver isozymes". The Journal of Biological ... Members of this family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, ...
Riboflavin kinase
McCormick DB; Butler RC (1962). "Substrate specificity of liver flavokinase". Biochim. Biophys. Acta. 65 (2): 326-332. doi: ... the two substrates of this enzyme are ATP and riboflavin, whereas its two products are ADP and FMN. Riboflavin is converted ...
Muscle atrophy
When a substrate is thus "poly-ubiquitinated", it is targeted for destruction by the proteasome. Particular enzymes in the ... ubiquitin/proteasome pathway allow ubiquitination to be directed to some proteins but not others - specificity is gained by ... are targeted for destruction by the ligation of at least four copies of a small peptide called ubiquitin onto a substrate ... coupling targeted proteins to an "E3 ubiquitin ligase". Each E3 ubiquitin ligase binds to a particular set of substrates, ...
Positron emission tomography
Nifene for nicotinic acetylcholine receptors or enzyme substrates (e.g. 6-FDOPA for the AADC enzyme). These agents permit the ... indirectly by competition studies between unlabeled drug and radiolabeled compounds known apriori to bind with specificity to ... used in PET imaging to determine the activity of the acetylcholinergic neurotransmitter system by acting as a substrate for ...
PSEN1
Tanahashi H, Tabira T (February 1999). "Isolation of human delta-catenin and its binding specificity with presenilin 1". ... and gamma-secretase substrates". Neurobiol. Dis. 14 (2): 194-204. doi:10.1016/S0969-9961(03)00123-2. PMID 14572442.. ...
2-alkenal reductase
"Antioxidative function and substrate specificity of NAD(P)H-dependent alkenal/one oxidoreductase. A new role for leukotriene B4 ... The 3 substrates of this enzyme are n-alkanal, NAD+, and NADP+, whereas its 4 products are alk-2-enal, NADH, NADPH, and H+. ...
Alan Hall
... showed the specificity of Rho in the stimulation of focal adhesions and stress fibres formation in fibroblasts in the ... By plating SCG on plastic dishes in presence of different substrates, Hall realised that Ral was activated by laminin to induce ... providing specificity.[10] In the same year, Hall investigated the role of the small GTPase Ral in neurite branching. After ... yet very little investigation into the way in which specificity of the pathway is maintained. It was known at this point that ...
MAP2K4
Dual specificity mitogen-activated protein kinase kinase 4 is an enzyme that in humans is encoded by the MAP2K4 gene. This gene ... 1999). "The mixed lineage kinase DLK utilizes MKK7 and not MKK4 as substrate". J. Biol. Chem. 274 (15): 10195-202. doi:10.1074/ ... 1996). "Eph receptors and ligands comprise two major specificity subclasses and are reciprocally compartmentalized during ... "Identification of a dual specificity kinase that activates the Jun kinases and p38-Mpk2". Science. 268 (5208): 286-90. doi: ...
Ionic liquid
They offer the specificity required to separate similar compounds from each other, such as separating polymers in plastic waste ... allowing for relatively easy separation of products and/or unreacted substrate(s). Gas solubility follows the same trend, with ...
Հեպարին - Վիքիպեդիա՝ ազատ հանրագիտարան
1990)։ «Examination of the substrate specificity of heparin and heparan sulfate lyases»։ Biochemistry 29 (10): 2611-2617։ PMID ... 1993)։ «Specificity studies on the heparin lyases from Flavobacterium heparinum»։ Biochemistry 32 (32): 8140-8145։ PMID 8347612 ... Evidence for an exosite determinant of factor Xa specificity in heparin-activated antithrombin»։ J. Biol. Chem. 276 (18): 14961 ... Chuang YJ, Swanson R. (2001)։ «Heparin enhances the specificity of antithrombin for thrombin and factor Xa independent of the ...
Proteasome
The proteasome assembled with these alternative subunits is known as the immunoproteasome, whose substrate specificity is ... It is therefore the E3 that confers substrate specificity to this system.[50] The number of E1, E2, and E3 proteins expressed ... and β5i with altered substrate specificity. The complex formed with the specialized β subunits is known as the immunoproteasome ... they have three distinct substrate specificities considered chymotrypsin-like, trypsin-like, and peptidyl-glutamyl peptide- ...
Innate immune system
Pathogen-specificity[edit]. The parts of the innate immune system have different specificity for different pathogens. ... "Induction of type I interferon by RNA viruses: cellular receptors and their substrates". Amino Acids. 38 (5): 1283-99. doi ...
효소 - 위키백과, 우리 모두의 백과사전
효소(酵素, 영어: enzyme)는 반응물인 기질(substrate)과 결합해서 효소-기질 복합체를 형성하여 화학 반응의 활성화 에너지 수준을 낮춤으로써 물질대사의 속도를 증가시키는 생체 촉매이거나 또는 속도를 조절하는 생체 ... "Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition" (PDF). 》PLoS ONE ... The naming of enzymes by adding the suffix "-ase" to the substrate on which the enzyme acts, has been traced to French ... 보호기능을 수행한다.[1] 효소는 기질(substrate)을 생성물(probuct)로 알려진 다른 분자로 전환시킨다. 세포의 거의 모든 대사 과정은 생명을 유지할 수 있을 만큼의 빠른 속도로 일어나야 하기 때문에 효소 촉매작용을 ...
Orizin
Esterase activity against N-acylated peptide ester substrates". Arch. Biochem. Biophys. 165: 72-79. PMID 4441086. ... Spadari, S., Subramanian, A.R. and Kalnitsky, G. (1974). "Highly restricted specificity of the serine proteinase ... Hayashi, K. and Terada, M. (1972). "Some characteristics of hydrolysis of synthetic substrates and proteins by the alkaline ...
Flea
In some species, the flea lives in the nest or burrow and the eggs are deposited on the substrate,[8] but in others, the eggs ... In general, host specificity decreases as the size of the host species decreases. Another factor is the opportunities available ...
Undekaprenilna difosfataza - Википедија, слободна енциклопедија
Touze, T., Blanot, D. and Mengin-Lecreulx, D. (2008). „Substrate specificity and membrane topology of Escherichia coli PgpB, an ...
Retinoid
The different hydrolyzing enzymes are activated by different types of bile salts and have distinct substrate specificities. For ...
Surface-enhanced Raman spectroscopy
An ideal SERS substrate must possess high uniformity and high field enhancement. Such substrates can be fabricated on a wafer ... Using antibodies and gold particles this approach can quantify proteins in serum with high sensitivity and specificity.[43] ... SERS substrates are used to detect the presence of low abundance biomolecules, and can therefore detect proteins in body fluids ... The ability to analyze the composition of a mixture on the nano scale makes the use of SERS substrates beneficial for ...
Glycosylation
... absence of glycosyltransferases which dictates which blood group antigens are presented and hence what antibody specificities ...
Phosphatidic acid
However, it is worth noting that in vitro, the various acyltransferases exhibit different substrate specificities with respect ... Whatever the mechanism is, such specificity is possible. It is seen in the pig testes DAGK that is specific for polyunsaturated ...
Phenethylamine
"The unique substrate specificity of human AOC2, a semicarbazide-sensitive amine oxidase". Cell. Mol. Life Sci. 66 (16): 2743-57 ... Wang X, Li J, Dong G, Yue J (February 2014). "The endogenous substrates of brain CYP2D". Eur. J. Pharmacol. 724: 211-218. doi: ... The preferred in vitro substrates of AOC2 were found to be 2-phenylethylamine, tryptamine and p-tyramine instead of methylamine ... β-PEA would not be deaminated in the gut as it is a selective substrate for MAO-B which is not found in the gut .... Brain ...
Anti-nuclear antibody
The lack of other nuclear antigens in this organelle means that using C.luciliae as a substrate allows for the specific ... Some ANAs appear in several types of disease, resulting in lower specificity of the test. For example, IgM-rheumatoid factor ( ... Typically, HEp-2 cells are used as a substrate to detect the antibodies in human serum. Microscope slides are coated with HEp-2 ... They are used as a substrate in immunofluorescence for the detection of anti-dsDNA antibodies. They possess an organelle known ...
Aminoacyl tRNA synthetase
Most of the aaRSs of a given specificity are evolutionarily closer to one another than to aaRSs of another specificity. However ... leucyl-tRNA synthetase from Thermus thermophilus complexed with a post-transfer editing substrate analogue ... Most of the aaRSs of a given specificity also belong to a single class. However, there are two distinct versions of the LysRS ...
Prolilna oligopeptidaza - Википедија, слободна енциклопедија
Nomura, K. (1986). „Specificity of prolyl endopeptidase". FEBS Lett. 209: 235-237. PMID 3539636.. ... Moriyama, A., Nakanishi, M. and Sasaki, M. (1988). „Porcine muscle prolyl endopeptidase and its endogenous substrates". J. ...
Histone methyltransferase
The C-terminal is important for the substrate specificity and binding of Dot1 because the region carries a positive charge, ... Cofactor binding and substrate interactions". J. Biol. Chem. 275 (5): 3128-36. doi:10.1074/jbc.275.5.3128. PMID 10652296.. ... In order for the reaction to proceed, S-Adenosyl methionine (SAM) and the lysine residue of the substrate histone tail must ... The catalytic domain of PRMTs consists of a SAM binding domain and substrate binding domain (about 310 amino acids in total).[5 ...
Protein
... s can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of ... although the surrounding amino acids may determine the exact binding specificity). A large number of such motifs has been ... The molecules bound and acted upon by enzymes are called substrates. Although enzymes can consist of hundreds of amino acids, ... To scale in the top right-hand corner are two of its substrates, ATP and glucose. ...
Fungicide
The pathogen had five ABC-type transporters with overlapping substrate specificities that together work to pump toxic chemicals ...
Enzyme - Simple English Wikipedia, the free encyclopedia
This complex is called an enzyme-substrate complex. For example, sucrase, 400 times the size of its substrate sucrose, splits ... "Application of a theory of enzyme specificity to protein synthesis". Proc. Natl. Acad. Sci. 44 (2): 98-104. doi:10.1073/pnas. ... Substrate + Enzyme -, Substrate:Enzyme -, Product:Enzyme -, Product + Enzyme. Enzymes lower the activation energy of a reaction ... This prevents or slows down an enzyme-substrate complex being formed. Denaturation[change , change source]. Denaturation is the ...
Ubiquitin-conjugating enzyme
The E3 molecules responsible for substrate identification and binding are thus the mechanisms of substrate specificity in ... The E3 molecule is responsible for binding the target protein substrate and transferring the ubiquitin from the E2 cysteine to ...
Complement component 1s
Skoog MT, Mehdi S, Wiseman JS, Bey P (June 1989). "The specificity of two proteinases that cleave adjacent to arginine, C1 ... esterase and acrosin, for peptide p-nitroanilide substrates". Biochimica et Biophysica Acta. 996 (1-2): 89-94. doi:10.1016/0167 ...
Coeliac disease
Role of enzyme specificity and pH influence on the transamidation versus deamidation process". J Biol Chem. 277 (37): 34109- ... Skovbjerg H, Norén O, Anthonsen D, Moller J, Sjöström H (2002). "Gliadin is a good substrate of several transglutaminases: ... However, five findings have been associated with a high specificity for coeliac disease: scalloping of the small bowel folds ( ... Do sensitivity and specificity vary in different populations?" (PDF). Gastroenterology. 128 (4 Suppl 1): S25-32. doi:10.1053/j. ...
P110α
insulin receptor substrate binding. • ATP binding. • 1-phosphatidylinositol-3-kinase activity. • phosphatidylinositol-4,5- ... 2.7.12: protein-dual-specificity. *see serine/threonine-specific protein kinases. 2.7.13: protein-histidine. *Protein-histidine ...
Molecular determinants of metalloproteinase substrate specificity | SpringerLink
Molecular determinants of metalloproteinase substrate specificity. Matrix metalloproteinase substrate binding domains, modules ... substrate specificity, and tissue inhibitor of metalloproteinase interaction. J. Biol. Chem. 272, 7608-7616.PubMedCrossRef ... cDNA cloning and deprivation of protein substrate specificity by autolytic degradation. Biochemistry 36, 7225-7238.PubMed ... identification of regions responsible for substrate specificity and general proteinase activity. Proc. Natl. Acad. Sci. USA. 90 ...
Redesigning trypsin: alteration of substrate specificity. - PubMed - NCBI
... they showed enhanced substrate specificity relative to the native enzyme. This increased specificity was achieved by the ... Redesigning trypsin: alteration of substrate specificity.. Craik CS, Largman C, Fletcher T, Roczniak S, Barr PJ, Fletterick R, ... Computer graphic analysis suggested that these substitutions would differentially affect arginine and lysine substrate binding ... at position 226 exhibited an altered conformation that may be converted to a trypsin-like structure upon binding of a substrate ...
Determinants for Substrate Specificity of Protein Phosphatase 2A
Substrate specificity of RdgB protein, a deoxyribonucleoside triphosphate pyrophosphohydrolase. - PubMed - NCBI
Kinetic analysis reveals that the major source of the substrate specificity lies in changes in K(m) for the various substrates ... Substrate specificity of RdgB protein, a deoxyribonucleoside triphosphate pyrophosphohydrolase.. Burgis NE1, Cunningham RP. ... possess deoxyribonucleoside triphosphate pyrophosphohydrolase activity and that all four RdgB homologs have high specificity ...
Substrate specificity and mismatch discrimination in DNA ligases | NEB
The specificity and accuracy of the ligation depends upon ligase selection and careful optimization of reaction conditions. ... Substrate specificity and mismatch discrimination in DNA ligases. by Greg Lohman, Ph.D., New England Biolabs, Inc.. DNA ligases ... Ligase Specificity. DNA ligases generally prefer fully Watson-Crick base-paired dsDNA substrates to those containing one or ... Home Tools & Resources Feature Articles Substrate specificity and mismatch discrimination in DNA ligases ...
Structural basis of substrate specificity in the serine proteases
Structure-based mutational analysis of serine protease specificity has produced a large database of information useful in ... Structural basis of substrate specificity in the serine proteases Protein Sci. 1995 Mar;4(3):337-60. doi: 10.1002/pro. ... Critical issues examined include the function of water molecules in providing strength and specificity of binding, the extent ... Structure-based mutational analysis of serine protease specificity has produced a large database of information useful in ...
Understanding the substrate specificity of conventional calpains
Cys proteases that play important roles in a wide range of biological phenomena via the limited proteolysis of their substrates ... substrate specificities, including a preference for sequences over secondary structures and the existence of a substrate ... Understanding the substrate specificity of conventional calpains Biol Chem. 2012 Sep;393(9):853-71. doi: 10.1515/hsz-2012-0143 ... The full spectrum of this substrate specificity, however, has not been clarified using standard sequence analysis algorithms, e ...
WikiGenes - Substrate Specificity
Anatomical context of Substrate Specificity. *The strict substrate specificity of this reaction suggests that L-arginine is the ... Gene context of Substrate Specificity. *The substrate specificity of the truncated RAD2 protein implicates branched DNA ... Disease relevance of Substrate Specificity. *Altered substrate specificity of herpes simplex virus thymidine kinase confers ... Substrate specificity and affinity of a protein modulated by bound water molecules. Quiocho, F.A., Wilson, D.K., Vyas, N.K. ...
188af) Exploring and Enhancing the Activity and Substrate Specificity of Amine Dehydrogenases | AIChE
188af) Exploring and Enhancing the Activity and Substrate Specificity of Amine Dehydrogenases. ... have increased activity across the board without affecting substrate. specificity. Finally, we have demonstrated for the first- ... chimeric amine dehydrogenase shows altered substrate specificity compared to. its parent enzymes. Chem Commun. (Camb) 2014, 50 ... ammonia, ketone, and NADH as substrates and release an (R)-amine, NAD+,. and water as products as seen in the reaction scheme ...
A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity | Science
A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity. By Chava Kimchi-Sarfaty, Jung Mi Oh, In-Wha Kim, Zuben ... A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity. By Chava Kimchi-Sarfaty, Jung Mi Oh, In-Wha Kim, Zuben ... A Silent Polymorphism in the MDR1 Gene Changes Substrate Specificity Message Subject. (Your Name) has forwarded a page to you ... mammalian membrane transport protein alters the substrate specificity. We hypothesize that when frequent codons are changed to ...
Use of PEPscreen® Peptides to Investigate Protein Farnesyltransferase Substrate Specificity | Sigma-Aldrich
Peptide substrate specificity also depends on interactions of the peptide with the FPP co-substrate 28-30. As these findings ... These results improve the definition of prenyltransferase substrate specificity, test the efficacy of substrate algorithms, and ... Biochemical studies of prenyltransferase substrate specificity indicate that recognition of peptide substrates is more complex ... the MTO substrates, the STO substrates, and the non-substrate peptides. Wedges are labeled with the percentage representation ...
Furaldehyde substrate specificity and kinetics of Saccharomyces cerevisiae alcohol dehydrogenase 1 variants
... Laadan, B. ... resulting in Adh1p-variants with different substrate specificities. ... Kinetic characterization with both aldehydes and the in vivo primary substrate acetaldehyde also enabled to correlate the ... of both native and mutated ADH1 genes was performed in order to identify the key amino acids involved in this substrate shift, ...
Diversity and Substrate Specificity in the Structures of Steroidogenic Cytochrome P450 Enzymes
Analysis of AtZDP substrate specificity
Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. | PNAS
Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition.. E Pizzi, ... Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. ... Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. ... Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. ...
Chemoenzymatic synthesis of prodigiosin analogues-exploring the substrate specificity of PigC - Chemical Communications (RSC...
RCSB PDB - 1ABF: SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES
Substrate specificity and affinity of a protein modulated by bound water molecules.. Quiocho, F.A., Wilson, D.K., Vyas, N.K.. ( ... SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES. *DOI: 10.2210/pdb1ABF/pdb ... can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding ...
RCSB PDB - 1BWP: PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
Thr103 and Leu194 indeed contribute to substrate specificity and in addition suggest that the integrity of the specificity ... Probing the Substrate Specificity of the Intracellular Brain Platelet-Activating Factor Acetylhydrolase. Ho, Y.S., Sheffield, P ... PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE. *DOI: 10.2210/pdb1BWP/ ... PAF-AH at 1.7 A resolution paved the way for a detailed examination of the molecular basis of substrate specificity in this ...
Substrate specificity of protein kinases - Patent # 5532167 - PatentGenius
The invention also provides peptide substrates for protein kinase A, cell cycle control kinases, src family kinases, the EGF ... peptides within the library which are substrates for the kinase are converted to phosphopeptides and the phosphopeptides are ... When the substrate is a substrate for a protein-serine/threonine kinase, Xaa5 is Ser or Thr, whereas whenthe substrate is a ... This invention pertains to the substrate specificity of protein kinases and to peptides which are substrates for protein ...
Substrate Specificity of the Escherichia coli Outer Membrane Protease OmpT | Journal of Bacteriology
In this work we employed a novel version of substrate phage display (21) to analyze the extended substrate specificity of OmpT ... We have analyzed the substrate specificity of OmpT by two complementary substrate filamentous phage display methods: (i) in ... Substrate Specificity of the Escherichia coli Outer Membrane Protease OmpT. John D. McCarter, Daren Stephens, Kevin Shoemaker, ... Substrate Specificity of the Escherichia coli Outer Membrane Protease OmpT. John D. McCarter, Daren Stephens, Kevin Shoemaker, ...
Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr. | Journal of Bacteriology
Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr.. K A Klyachko, S Schuldiner, A A ... Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr.. K A Klyachko, S Schuldiner, A A ... Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr.. K A Klyachko, S Schuldiner, A A ... Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr. Message Subject (Your Name) has ...
Crystal structure of the FTO protein reveals basis for its substrate specificity. | Sigma-Aldrich
Substrate Specificity - Semantic Scholar
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule ... Substrate Specificity. Known as: Specificities, Substrate, Specificity, Substrate, Substrate Specificities A characteristic ... Studies of the substrate specificity, enzyme-substrate interactions, and the function of lipid. ... Substrate specificity and redox potential of AhpC, a bacterial peroxiredoxin.. *Derek Parsonage, P. Andrew Karplus, Leslie B. ...
The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity.
... Ilari A., ... Accordingly, a 15 fold increase in k(cat) and 100 fold decrease in K(m) for sarcosine as substrate has been achieved in MTOX ... The analysis of the substrate binding site highlights the structural determinants that favour the accommodation of the bulky N- ... located at the entrance of the active site appears to play a key role for the recognition of the amino acid substrate side ...
The Akt1-eNOS Axis Illustrates the Specificity of Kinase-Substrate Relationships in Vivo | Science Signaling
The Akt1-eNOS Axis Illustrates the Specificity of Kinase-Substrate Relationships in Vivo ... The Akt1-eNOS Axis Illustrates the Specificity of Kinase-Substrate Relationships in Vivo ... The Akt1-eNOS Axis Illustrates the Specificity of Kinase-Substrate Relationships in Vivo ... The Akt1-eNOS Axis Illustrates the Specificity of Kinase-Substrate Relationships in Vivo ...
Substrate Specificity of Acyl-Lipid Δ9-Desaturase from Cyanobacterium sp. IPPAS B-1200, a Cyanobacterium with Unique Fatty Acid...
Substrate Specificity of Acyl-Lipid Δ9-Desaturase from Cyanobacterium sp. IPPAS B-1200, a Cyanobacterium with Unique Fatty Acid ... We cloned this gene and characterized its specificity to the length of the substrate using heterologous expression in Escheri ... Substrate specificity of acyl-lipid Δ9-desaturase from Prochlorothrix hollandica cyanobacterium producing myristoleic acid, ...
Novel IgG-Degrading Enzymes of the IgdE Protease Family Link Substrate Specificity to Host Tropism of Streptococcus Species
... thereby linking the substrate specificity to the known host tropism. The novel IgdE family proteases of S. agalactiae, S. ... Porcine IgG subtype specificities of the IgdE family proteases of S. porcinus and S. pseudoporcinus remain to be determined. ... The IgG subtype specificity of bacterial proteases indicates the special importance of these IgG subtypes in counteracting ... pseudoporcinus and S. equi showed IgG subtype specificity, i.e. IgdE from S. agalactiae and S. pseudoporcinus cleaved human ...
Substrate specificity of glutamyl endopeptidase (GE): hydrolysis studies with a bovine α-casein preparation. | UL - University...
Substrate specificity of glutamyl endopeptidase (GE): hydrolysis studies with a bovine α-casein preparation. Kalyankar P, Zhu Y ... Substrate specificity of glutamyl endopeptidase (GE): hydrolysis studies with a bovine α-casein preparation. in Food Chemistry ... Home , Substrate specificity of glutamyl endopeptidase (GE): hydrolysis studies with a bovine α-casein preparation. ...
Insights into substrate specificity of NlpC/P60 cell wall hydrolases containing bacterial SH3 domains (Journal Article) | DOE...
... and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity ... To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and ... Title: Insights into substrate specificity of NlpC/P60 cell wall hydrolases containing bacterial SH3 domains ... Accepted Manuscript: Insights into substrate specificity of NlpC/P60 cell wall hydrolases containing bacterial SH3 domains ...
Dissertations.se: SUBSTRATE SPECIFICITY SWITCH
... about SUBSTRATE SPECIFICITY SWITCH. Search and download thousands of Swedish university dissertations. Full text. Free. ... substrate specificity switch. Showing result 1 - 5 of 7 swedish dissertations containing the words substrate specificity ... Keywords : NATURVETENSKAP; NATURAL SCIENCES; Yersinia; type III secretion; YscU; substrate specificity switch; heat shock ... Substrate specificity; Biotechnology; Bioteknologi; Abstract : Biocatalysis is an ever evolving field that uses enzymes or ...
EnzymesResiduesPeptideCatalyticRecognitionInhibitorCleavageDifferences in substrate specificityEscherichiaInhibitorsAltered substrate specificity comparedProteinsInsight into the substrate specificityAlter substrate specificityExtreme substrate specificityChanges Substrate SpecificitySpecific SubstratesCharacterizationDistinctBroad specificityMolecularKineticsMutationsDeterminantsSelectivityProteaseMechanismKinasesAcceptorStructuralWide range of substratesNicked substrates that containSynthesisPeptidesInteractionsBacterialKineticGeneEnzymaticVitroAffinityMismatch discriminationArginineSubunitHigh specificityFluorescent substratesAssayAmino acidsProteasesConformational changesResiduePhosphorylationSequencePhysiologicalPreferentiallyAssaysHydrolysisProbingSingle amino acid
Enzymes23
- Although the mutant enzymes were reduced in catalytic rate, they showed enhanced substrate specificity relative to the native enzyme. (nih.gov)
- Bommarius, A. S., A novel chimeric amine dehydrogenase shows altered substrate specificity compared to its parent enzymes. (aiche.org)
- The exquisite substrate specificity of Dus enzymes is therefore controlled by a relatively simple mechanism involving major reorientation of the whole tRNA molecule. (uniprot.org)
- In addition, these enzymes all have γ-d-Glu-A 2 pm (A 2 pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. (osti.gov)
- Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. (osti.gov)
- To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. (osti.gov)
- Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. (osti.gov)
- The broad specificity of these enzymes makes them amenable for designing prodrugs. (aspetjournals.org)
- To facilitate their biocatalytic exploitation, it is important to develop methods by which variants of the enzymes can be rapidly screened for increased activity towards substrates of interest. (mdpi.com)
- DUB activity is usually assayed using full-length ubiquitin, and these enzymes generally show low activity towards small substrates that constitute the P4-P1 LRGG (Lys-Arg-Gly-Gly) C-terminal motif of ubiquitin. (portlandpress.com)
- Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes. (elifesciences.org)
- To overcome this limitation, we propose to use a bifunctional enzyme to study the evolution of substrate specificity after gene loss, as these enzymes may continue to operate when only one of their associated metabolic pathways becomes dispensable. (elifesciences.org)
- Kinetic and inhibitor studies using cDNA-expressed enzymes and human liver microsomes have characterized the specificity of a range of cytochrome P450 (CYP) 1A substrate and inhibitor probes towards the two isoforms comprising this subfamily. (aspetjournals.org)
- Identification and further prioritizing new substrates are important for the study of the enzymology of the selected enzymes and the next generation of drug targets ( 4 ). (mcponline.org)
- Substrate specificities of these enzymes are discussed, along with structure-function relationships, based on their crystal structures and homology modeling. (frontiersin.org)
- The enzymes were tested for their substrate preference towards chitin, lipo-chitooligosaccharide Nod factors of Rhizobium, and bacterial peptidoglycans (lysozyme activity) as well as for their capacity to inhibit hyphal growth of Trichoderma viride. (deepdyve.com)
- Patterns of substrate affinity showed that Leu-AMC (at both sampling sites) and Arg-AMC (at Bogue Sound) were primarily hydrolyzed by enzymes other than leucyl-aminopeptidase and arginyl-aminopeptidase, respectively. (darkenergybiosphere.org)
- In vitro assays for N-acetylgalactosaminyl transferase and glucuronosyl transferase II were developed and utilized to determine kinetic parameters which define the substrate specificity of the enzymes toward a series of different ('3)H-oligosaccharide substrates. (illinois.edu)
- How do these enzymes, which all appear to share a common terpene synthase fold, specify the many different products made almost entirely from one of only three substrates? (plantcell.org)
- Elucidation of the structure of 1,8-cineole synthase from Salvia fruticosa (Sf - CinS1) combined with analysis of functional and phylogenetic relationships of enzymes within Salvia species identified active-site residues responsible for product specificity. (plantcell.org)
- Glycoside hydrolases of families 32 (GH32) and 68 (GH68) belong to clan GH-J, containing hydrolytic enzymes (sucrose/ fructans as donor substrates) and fructosyltransferases (sucrose/fructans as donor and acceptor substrates). (kuleuven.be)
- Based on the available 3D structures of enzymes and enzyme-ligand complexes as well as docking simulations, we calculated the pKa of the acid-base before and after substrate binding. (kuleuven.be)
- The binding of substrates to heme enzymes has been widely assumed to occur at the so-called delta-heme edge. (le.ac.uk)
Residues12
- In this model, "C" refers to a cysteine three residues removed from the C-terminus that is prenylated at the thiol group to form a thioether, "a" refers to any aliphatic amino acid, and "X" refers to a subset of amino acids that are proposed to determine specificity for FTase (methionine, serine, glutamine, alanine) or GGTase-I (leucine, phenylalanine). (sigmaaldrich.com)
- These results are consistent with the model in which residues Leu48, Thr103 and Leu194 indeed contribute to substrate specificity and in addition suggest that the integrity of the specificity pocket is critical for the expression of full catalytic function, thus conferring very high substrate selectivity on the enzyme. (rcsb.org)
- OmpT and its homologues cleave synthetic substrates between dibasic residues with high catalytic efficiency ( 14 , 19 , 30 ). (asm.org)
- Here we demonstrate that various substitutions of residues Phe143 and Phe306 of Bmr not only reduce its sensitivity to reserpine inhibition but also significantly change its substrate specificity. (asm.org)
- This result strongly suggests that Bmr interacts with its transported drugs directly, with residues Phe143 and Phe306 likely to be involved in substrate recognition. (asm.org)
- Role of multiple basic residues in determining the substrate specificity of cyclic AMP-dependent protein kinase. (semanticscholar.org)
- In fact, although the nature and geometry of the catalytic residues within the first contact shell of the FAD moiety appear to be virtually superposable in MTOX and MSOX, the presence of a Thr residue in position 239 in MTOX (Met245 in MSOX) located at the entrance of the active site appears to play a key role for the recognition of the amino acid substrate side chain. (uniprot.org)
- Thereafter, insects lost all but one kinase, dNK (EC 2.7.1.145), which subsequently, through remodelling of a limited number of amino acid residues, gained a broad substrate specificity. (ruc.dk)
- Results: Using a combination of peptide library selection, phosphorylation of opitmal peptide variants, and screening of a phosphosite array, we found that Dbf2-Mob1 preferentially phosphorylated serine over threonine and required an arginine three residues upstream of the phosphorylated serine in its substrate. (caltech.edu)
- The critical acidic residues are conserved in plants and animals with the corresponding mutations impairing the enzyme activity of both JMJ14 and human KDM5B, indicating a common substrate recognition mechanism for KDM5 subfamily demethylases shared by plants and animals and further informing efforts to design targeted inhibitors of human KDM5. (plantcell.org)
- PepB is a broad specificity aminopeptidase with a unique ability to remove Asp residues and a very efficient ability to remove Glu residues from the N-termini of peptides in than PepA and PepN. (illinois.edu)
- In contrast replacing a small cassette of residues 338-341 produced a small increase in the specificity factor. (lancs.ac.uk)
Peptide14
- Based on comparison of known prenylated proteins, both FTase and GGTase-I have been proposed to recognize protein or peptide substrates containing a C-terminal "Ca 1 a 2 X" sequence 11-17 . (sigmaaldrich.com)
- 1992) "Synthetic Peptide Libraries in the Determination of T Cell Epitopes and Peptide Binding Specificity of Class I Molecules" Eur. (patentgenius.com)
- 1991) "Peptide-Binding Specificity of the Molecular Chaperone BiP" Nature 353:726-730. (patentgenius.com)
- In the method of the invention, a protein kinase is contacted with an oriented degenerate peptide library, peptides within the library which are substrates for the kinase are converted to phosphopeptides and the phosphopeptides are separated from non-phosphorylated peptides. (patentgenius.com)
- The invention also provides peptide substrates for protein kinase A, cell cycle control kinases, src family kinases, the EGF receptor and p92.sup.c-fps/fes based upon amino acid sequence motifs for the phosphorylation sites of these kinases. (patentgenius.com)
- When coupled with high-throughput quantitative proteomics technique, this simplified model enabled the accurate determination of catalytic efficiencies for 2369 peptide substrates of a protease by using only one enzymatic reaction experiment. (mcponline.org)
- Highly complex substrate libraries including the synthetic oligonucleotide or peptide mixture ( 9 , 10 ), the peptide library derived from the digestion of proteins in total cell lysate ( 11 , 12 ) and the proteins in total cell lysate ( 13 , 14 ) were used for substrate screening. (mcponline.org)
- This requirement for arginine in peptide substrates could not be substituted with the similarly charged lysine. (caltech.edu)
- This specificity determined for peptide substrates was also evident in many of the proteins phosphorylated by Dbf2-Mob1 in a proteome chip analysis. (caltech.edu)
- Conclusion: We have determined by peptide library selection and phosphosite array screening that the protein kinase Dbf2-Mob1 preferentially phosphorylated substrates that contain an RXXS motif. (caltech.edu)
- Direct insights into substrate binding and catalytic mechanism of an intramembrane protease now come from X‐ray structures of the bacterial rhomboid protease GlpG complexed to substrate‐derived peptide inhibitors. (embopress.org)
- To address these interesting observations, we have synthesized a library of substrates containing different peptide scaffolds functionalized with a number of N - ε -acyl moieties. (dtu.dk)
- We report a systematic analysis of the P1 and P2 substrate specificity of TNF-α converting enzyme (TACE) using a peptide library and a novel analytical method, and we use the substrate specificity information to design novel reverse hydroxamate inhibitors. (eurekaselect.com)
- Based on this result, 1000 different peptide substrates of the form Biotin-LAQA-P1-P2- SSK(DNP)-NH2 were prepared, with 50 different natural and unnatural amino acids at P1 in combination with 20 different amino acids at P2. (eurekaselect.com)
Catalytic11
- The importance of discrete MMP substrate binding sites termed exosites on domains located outside the catalytic domain was first demonstrated for native collagenolysis. (springer.com)
- This increased specificity was achieved by the unexpected differential effects on the catalytic activity toward arginine and lysine substrates. (nih.gov)
- The recent solution of the crystal structure of the alpha(1) catalytic subunit of isoform Ib of bovine brain intracellular PAF-AH at 1.7 A resolution paved the way for a detailed examination of the molecular basis of substrate specificity in this enzyme. (rcsb.org)
- A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts. (semanticscholar.org)
- Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. (osti.gov)
- Based on this striking observation, a simplified model was developed to determine the catalytic efficiencies of numerous competing substrates presented in the complex enzyme reaction system. (mcponline.org)
- A study of substrate-inhibitor specificity of mitochondrial monoamine oxidase (MAO) in the hepatopancreas of the adult Kamchatka crab Paralithodes camtschaticus revealed specific catalytic properties of the enzyme. (springer.com)
- Here, we show that Sin1 is dispensable for the catalytic activity of TORC2, but its conserved region in the middle (Sin1CRIM) forms a discrete domain that specifically binds the TORC2 substrate kinases. (elifesciences.org)
- Substrate structure may explain the catalytic efficiencies observed. (caltech.edu)
- Here, we report the crystal structures of the JMJ14 catalytic domain in both substrate-free and bound forms. (plantcell.org)
- The obtained results strongly suggest that most GH-J members show an acid-base catalyst that is not sufficiently protonated before ligand entrance, while the acid-base can be fully protonated when a substrate, but not an inhibitor, enters the catalytic pocket. (kuleuven.be)
Recognition13
- This article updates a previous review of the role of substrate recognition by MMP exosites in both preparing complex substrates, such as collagen, for cleavage and for tethering noncollagenous substrates to MMPs for more efficient proteolysis. (springer.com)
- Studies show that certain sequence preferences influence calpain substrate recognition, and some properties of amino acids have been related successfully to substrate specificity and to the calpains' 3D structure. (nih.gov)
- Such reprogramming of the enzymatic specificity appears to be a unique evolutionary solution for altering tRNA recognition by the same protein fold. (uniprot.org)
- Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. (pnas.org)
- The crystal structure suggests that the side chains of Thr103, Leu48 and Leu194 are involved in substrate recognition. (rcsb.org)
- The understanding of the molecular mechanisms of LC/F substrate recognition provides insights into the development of antitoxins and engineering novel BoNTs to optimize current therapy and extend therapeutic interventions. (biochemj.org)
- Together with previous data, the results indicate that the majority of human CYP1A xenobiotic inhibitor and substrate probes are nonspecific in their recognition of CYP1A1 and CYP1A2, although selectivity is apparent for some compounds. (aspetjournals.org)
- To date, the details of substrate recognition and catalysis by FUT8 remain unknown. (sebbm.es)
- Here, we report the crystal structure of FUT8 complexed with GDP and a biantennary complex N -glycan ( G0 ), which provides insight into both substrate recognition and catalysis. (sebbm.es)
- The specific substrate-recognition function is conserved in human Sin1CRIM, which may represent a potential target for novel anticancer drugs that prevent activation of the mTORC2 substrates such as AKT. (elifesciences.org)
- The structures reveal that the jumonji and C5HC2 domains contribute to the specific recognition of the H3R2 and H3Q5 to facilitate H3K4me3 substrate specificity. (plantcell.org)
- Chemistry was successfully developed to replace the phosphate with a sulphonamide, but the compound was neither a substrate or an inhibitor, confirming the importance of the phosphate for molecular recognition. (lancs.ac.uk)
- In order to elucidate the mechanism of substrate recognition by CaMKPase, we chemically synthesized a variety of phosphopeptide analogs and carried out kinetic analysis using them as CaMKPase substrates. (semanticscholar.org)
Inhibitor13
- We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites. (sciencemag.org)
- 1991) "Protein Kinase C Substrate and Inhibitor Characteristics of Peptides Derived From the Myristoylated Alanine-Rich C Kinase Substrate (MARCKS) Protein Phosphorylation Site Domain" The Journal of Biological Chemistry266(22):14390-14398. (patentgenius.com)
- To this end, we developed and characterized a new mouse Abcg2-expressing subline that demonstrated efflux of known fluorescent ABCG2 substrates and increased resistance to mitoxantrone, which is reduced in the presence of the ABCG2 inhibitor Ko143. (aspetjournals.org)
- The similarity of the substrate and inhibitor specificity of human and mouse ABCG2 supports interpretation of mouse models in understanding the clinical, pharmacological, and physiologic roles of ABCG2. (aspetjournals.org)
- Specificity of substrate and inhibitor probes for human cytochromes P450 1A1 and 1A2. (aspetjournals.org)
- The prototypic CYP1A xenobiotic inhibitor and substrate probes alpha-naphthoflavone, ellipticine, 7-ethoxycoumarin and 7-ethoxyresorufin all inhibited CYP1A1- and CYP1A2-mediated phenacetin O-deethylation as well as the high-affinity component of human liver phenacetin O-deethylase activity. (aspetjournals.org)
- Despite valuable insights from inhibitor‐bound rhomboid proteases, full understanding of intramembrane proteolysis requires structural views of protease‐substrate complexes. (embopress.org)
- Structures of inhibitor‐bound complexes reveal the S1 to S4 subsites and explain GlpG substrate specificity. (embopress.org)
- However, this compound became sensitive to the stereochemistry of the glycoside linkage (the β-anomer was neither substrate or inhibitor) and the structure of the lipid moiety (the hexadecyl derivatives were inhibitors). (lancs.ac.uk)
- We also replaced the glucosamine by an acyclic analogue, but this also was inactive, both as a substrate and inhibitor. (lancs.ac.uk)
- These findings add significantly to our understanding of substrate and inhibitor binding to the GlcNAc-PI de-N-acetylase enzyme and will have a bearing on the design of future inhibitors. (lancs.ac.uk)
- Lirias: pKa modulation of the acid/base catalyst within GH32 and GH68: a role in substrate/inhibitor specificity? (kuleuven.be)
- This provides a new mechanistic insight aiming at understanding the complex substrate and inhibitor specificities observed within the GH-J clan. (kuleuven.be)
Cleavage10
- The essential role of hemopexin carboxyl-domain exosites in the cleavage of noncollagenous substrates such as chemokines has also been recently revealed. (springer.com)
- The potential role of collagen binding in regulating MMP-2 (gelatinase A) activation at the cell surface reveals unexpected consequences of substrate interactions that can lead to collagen cleavage and regulation of the activation and activity of downstream proteinases necessary to complete the collagenolytic cascade. (springer.com)
- More advanced bioinformatics techniques were used recently to identify the substrate specificities of calpains and to develop a predictor for calpain cleavage sites, demonstrating the potential of combining empirical data acquisition and machine learning. (nih.gov)
- We have analyzed the substrate specificity of OmpT by two complementary substrate filamentous phage display methods: (i) in situ cleavage of phage that display protease-susceptible peptides by Escherichia coli expressing OmpT and (ii) in vitro cleavage of phage-displayed peptides using purified enzyme. (asm.org)
- An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. (uniprot.org)
- Defining the physiological targets of a MazF toxin first requires the identification of its cleavage specificity, yet the current toolkit is antiquated and limited. (uniprot.org)
- We describe a rapid genome-scale approach, MORE (mapping by overexpression of an RNase in Escherichia coli) RNA-seq, for defining the cleavage specificity of endoribonucleolytic toxins. (uniprot.org)
- This work included chemical relaxation of specificities towards very frequent cleavage of DNA by Tsp GWI (Zylicz-Stachula et al. (springer.com)
- While the relaxed cleavage was not as intense as in the previous cases, we discovered and characterised the inherent Secondary-Cognate-Specificity (SCS) of Tso I, which is further highly stimulated by the presence of SAC-an analogue, which is not a methyl group donor, thus can be considered both an analogue of the reaction product-S-adenosyl-homocysteine (SAH) and the cofactor SAM. (springer.com)
- Other endoglycosidases, similar to PNGase F, include endoglycosidase F1, endoglycosidase F2, endoglycosidase F3, and endoglycosidase H. These endoglycosidases have more specificity in cleavage and are less sensitive to protein conformation than PNGase F. All of these endoglycosidases, including PNGase F, can be purified from an almond emulsion or flavobacterium meningosepticum. (wikipedia.org)
Differences in substrate specificity2
- To investigate the fundamental differences in substrate specificity between BMO and MMO, single amino acid substitutions were made to the hydroxylase α-subunit of BMO (BMOH-α). (oregonstate.edu)
- The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase), and UDP- N -acetyl glucosamine pyrophosphorylase (UAGPase), which can be distinguished both by their amino acid sequences and by differences in substrate specificity. (frontiersin.org)
Escherichia2
- To assess the origin of specificity of Escherichia coli leucyl-tRNA synthetase (LeuRS) against the cognate aminoacylation product in editing, we followed binding and catalysis independently using cognate leucyl- and non-cognate norvalyl-tRNA Leu and their non-hydrolyzable analogues. (elsevier.com)
- To gain insight into substrate binding by rhomboid proteases, we have synthesised a series of novel peptidyl‐chloromethylketone (CMK) inhibitors and analysed their interactions with Escherichia coli rhomboid GlpG enzymologically and structurally. (embopress.org)
Inhibitors9
- HeLa cells expressing double- and triple-haplotype mutants also revealed results similar to those for the single mutants ( Fig. 1, A to C ). However, the P-gp inhibitors cyclosporin A (CsA) and verapamil (fig. S1) were less effective against all the substrates in cells expressing the double or triple haplotypes carrying C3435T relative to the wild type, the SNPs, or the haplotype that does not carry C3435T. (sciencemag.org)
- 1976) "Synthetic Hexapeptide Substrates and Inhibitors of 3':5'-Cyclic AMP-Dependent Protein Kinase" Proc. (patentgenius.com)
- Taken together, these results provide a structural basis for understanding FTO substrate-specificity, and serve as a foundation for the rational design of FTO inhibitors. (sigmaaldrich.com)
- Other putative human CYP1A xenobiotic substrates and inhibitors, including caffeine, 5- and 8-methoxypsoralen, nifedipine, paraxanthine, propranolol and theophylline similarly inhibited CYP1A1- and 1A2-catalyzed phenacetin O-deethylation and the high-affinity human liver phenacetin O-deethylase. (aspetjournals.org)
- 1. Substrate-specificity of the main protease of SARS coronavirus was systematically profiled at P5 to P3' positions, which provided insights into a rational design of peptidomimetic inhibitors. (hkmj.org)
- Additionally, we have characterized the kinetics governing the specificity and discrimination of several widely administered Nucleotide Reverse Transcriptase Inhibitors (NRTI's) used to combat HIV infection including 3TC (Lamivudine), FTC (Emtricitabine), and AZT (Zidovudine) for the wild-type polymerase and mutants with clinical resistance to these compounds. (utexas.edu)
- Peptidyl chloromethylketones are substrate‐mimicking, mechanism‐based inhibitors of rhomboid protease. (embopress.org)
- In GH32 members, some of the sugar substrates can also function as inhibitors, this regulatory aspect further adding to the complexity in enzyme functionalities within this family. (kuleuven.be)
- These substrate preferences were used in the design of novel reverse hydroxamate TACE inhibitors with phenethyl and 5-methyl-thiophene-methyl side-chains at P1, and threonine and nitro-arginine at P2. (eurekaselect.com)
Altered substrate specificity compared1
- The results show that CYP2D6.17 exhibits altered substrate specificity compared with CYP2D6.1 and CYP2D6.2. (pubfacts.com)
Proteins18
- Expanding upon the "Ca 1 a 2 X" box paradigm, bioinformatic analysis and biochemical studies of known substrates and related proteins indicate that sequences immediately upstream of the conserved cysteine residue may also play a role in substrate selectivity 8,18,19 . (sigmaaldrich.com)
- However, as the total complement of prenylated proteins is unknown, the FTase substrates responsible for FTI efficacy are not yet understood. (sigmaaldrich.com)
- Understanding the in vivo substrate selectivity of FTase and GGTase-I constitutes an important step towards characterizing the prenylated proteins involved in these pathways. (sigmaaldrich.com)
- To generate this library, we searched the human genome database for proteins that contain a cysteine four amino acids from the C-terminus as a minimal specificity requirement. (sigmaaldrich.com)
- 300 peptides screened, FTase catalyzed multipleturnover farnesylation of 106 peptides, consistent with the parent proteins serving as FTase substrates in vivo. (sigmaaldrich.com)
- These different classes of FTase substrates may reflect an unanticipated mechanism for regulating farnesylation, with potential impact on the localization, trafficking, and activity of prenylated proteins within the cell. (sigmaaldrich.com)
- 1990) "Identification of Major Nucleolar Proteins As Candidate Mitotic Substrates of cdc2 Kinase" Cell 60:791-801. (patentgenius.com)
- 2. Assay of jejunal transglutaminase activity with a variety of dietary proteins as acceptors showed high activity with gliadin, comparable with that of the standard substrate, dimethylcasein. (portlandpress.com)
- These proteins are enriched for RXXS motifs, and may include substrates that mediate the function of Dbf2-Mob1 in mitotic exit and cytokinesis. (caltech.edu)
- Conclusion/Significance: The good correlation with the FAEs substrate specificities that we have defined via our phylogenetic analysis not only suggests that FAEs are phylogenetically informative proteins but it is also a considerable step towards improved FAEs functional prediction. (chalmers.se)
- This study places us closer to understanding the complex task of accommodating multiple substrate specificities in proteins of the thioredoxin superfamily and underscores the general applicability of ligand-induced stability to probe substrate specificity. (diva-portal.org)
- Recent studies have highlighted lysine acetylation as a general post-translational modification (PTM), andagrowing list of non-histone proteins has been identified as substrates for the KDACs, thereby extending their potential impactoncellular function. (dtu.dk)
- In mammals, thirteen aquaporins (AQP0-12) have been characterized, but in lower vertebrates, such as fish, the diversity, structure and substrate specificity of these membrane channel proteins are largely unknown. (uib.no)
- The results are discussed in terms of our more general understanding of substrate oxidation across other heme proteins, and the emerging role of the heme propionates at the gamma-heme edge. (le.ac.uk)
- Ras subcellular localization defines extracellular signal-regulated kinase 1 and 2 substrate specificity through distinct utilization of scaffold proteins. (hud.ac.uk)
- We present evidence indicating that the underlying mechanism of this substrate selectivity is governed by the participation of different scaffold proteins that distinctively couple ERK1/2, activated at defined microlocalizations, to specific substrates. (hud.ac.uk)
- These results disclose an unprecedented spatial regulation of ERK1/2 substrate specificity, dictated by the microlocalization from which Ras signals originate and by the selection of specific scaffold proteins. (hud.ac.uk)
- The Walker A motif is best known for its presence in ATP- and GTP-binding proteins, and is also found in a variety of proteins with phosphorylated substrates. (wikipedia.org)
Insight into the substrate specificity1
- Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans. (nii.ac.jp)
Alter substrate specificity2
- Acquired mutations in the MXR/BCRP/ABCP gene alter substrate specificity in MXR/BCRP/ABCP-overexpressing cells. (semanticscholar.org)
- In light of the fact that mutations in Pgp derived from drug selection have been shown to alter substrate specificity (11) , the MXR/BCRP/ABCP mRNA from 11 cell lines was sequenced to determine whether mutations could explain the differing substrate specificities. (aacrjournals.org)
Extreme substrate specificity1
- This extreme substrate specificity of EaDAcT distinguishes it from all other MBOATs which typically catalyze the transfer of much longer acyl groups. (k-state.edu)
Changes Substrate Specificity1
- These results suggest that amino acid 482 has a crucial role in MXR/BCRP/ABCP function and that mutation of a single amino acid residue significantly changes substrate specificity, thus altering the drug resistance phenotype. (aacrjournals.org)
Specific Substrates1
- Binding sites that have been designed to interact quite strongly with specific substrates are unlikely to bind nonspecifically to other substrates. (uu.nl)
Characterization3
- Kinetic characterization with both aldehydes and the in vivo primary substrate acetaldehyde also enabled to correlate the alterations in substrate affinity with the different amino acid substitutions. (diva-portal.org)
- Vascular peroxidase 1 catalyzes the formation of hypohalous acids: characterization of its substrate specificity and enzymatic properties. (biomedsearch.com)
- Molecular Characterization and Substrate Specificity of Nitrobenzene Dioxygenase from Comamonas sp. (asm.org)
Distinct9
- Surprisingly, of the remaining peptides, 67 % were farnesylated under single-turnover conditions, suggesting that there are two classes of substrates for FTase with distinct reactivity profiles. (sigmaaldrich.com)
- Analysis of the sequence preferences for these two classes of substrates illustrates a significant difference in FTase selectivity for the multiple- and single-turnover substrates, with the multiple-turnover substrates adhering closely to the current Ca 1 a 2 X model for FTase selectivity while the singleturnover substrates show distinct sequence preferences. (sigmaaldrich.com)
- Neuronal palmitoyl acyl transferases exhibit distinct substrate specificity. (semanticscholar.org)
- Human paraoxonases (PON1, PON2, and PON3) are lactonases with overlapping and distinct substrate specificities. (semanticscholar.org)
- We have previously speculated that this architecture might enable the Firmicutes BY-kinases to interact with alternative activators, and thus account for the observed ability of these kinases to phosphorylate several distinct classes of protein substrates. (frontiersin.org)
- The relatively low degree of sequence restriction at the site of phosphorylation suggests that Dbf2 achieves specificity by docking its substrates at a site that is distinct from the phosphorylation site. (caltech.edu)
- The target of rapamycin (TOR) protein kinase forms multi-subunit TOR complex 1 (TORC1) and TOR complex 2 (TORC2), which exhibit distinct substrate specificities. (elifesciences.org)
- G262V, S121G, F218Y, and F218I improve conversion of type I substrates, whereas G262A and IMP-1 improve conversion of type II substrates, indicating two distinct evolutionary adaptations from IMP-6. (caltech.edu)
- Although these substrates resemble each other structurally, they are transported by distinct coupling mechanisms. (embopress.org)
Broad specificity1
- PNGase F lacks selectivity for outer carbohydrate structure, resulting in broad specificity, making it a useful tool for investigating glycoprotein structure and function. (wikipedia.org)
Molecular4
- The biodegradation of aromatic hydrocarbons and related compounds by aerobic bacteria is often initiated by multicomponent dioxygenase systems that catalyze the addition of both atoms of molecular oxygen to the substrate. (asm.org)
- Finally, using molecular dynamics, we generate a model of the Michaelis complex of the substrate bound in the active site of GlpG. (embopress.org)
- Structure‐based modeling and molecular dynamics simulations allow generating a model of the Michaelis complex with the substrate. (embopress.org)
- A substrate-inhibitory analysis with the use of deprenyl and chloroginyl provides an indirect evidence for the existence of a sole MAO molecular form in the Kamchatka crab hepatopancreas. (springer.com)
Kinetics1
- Because of the well-developed enzyme kinetics theories and assay methods, the screening for optimal substrates is often performed by using the in vitro enzymatic reaction system involving an enzyme and a substrate ( 5 ⇓ ⇓ - 8 ). (mcponline.org)
Mutations1
- Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr. (asm.org)
Determinants2
- The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity. (uniprot.org)
- The analysis of the substrate binding site highlights the structural determinants that favour the accommodation of the bulky N-methyltryptophan residue in MTOX. (uniprot.org)
Selectivity1
- Opposing mechanisms govern substrate selectivity in the synthetic and editing site. (elsevier.com)
Protease5
- Structure-based mutational analysis of serine protease specificity has produced a large database of information useful in addressing biological function and in establishing a basis for targeted design efforts. (nih.gov)
- We have built a model of the specificity pocket of the protease of hepatitis C virus on the basis of the known structures of trypsin-like serine proteases and of the conservation pattern of the protease sequences among various hepatitis C strains. (pnas.org)
- The model allowed us to predict that the substrate of this protease should have a cysteine residue in position P1. (pnas.org)
- Substrate preferences at P5 to P3 positions were important in enhancing the main protease activity. (hkmj.org)
- We show that peptidyl‐CMKs derived from the natural rhomboid substrate TatA from bacterium Providencia stuartii bind GlpG in a substrate‐like manner, and their co‐crystal structures with GlpG reveal the S1 to S4 subsites of the protease. (embopress.org)
Mechanism2
- We further established the critical role for the A76 3′-OH group of the tRNA Leu in post-transfer editing, which supports the substrate-assisted deacylation mechanism. (elsevier.com)
- Understanding the mechanism of action and substrate specificity of BoNTs is a prerequisite to develop antitoxin and novel BoNT-derived protein therapy. (biochemj.org)
Kinases4
- Bacterial protein-tyrosine kinases (BY-kinases) are known to regulate different aspects of bacterial physiology, by phosphorylating cellular protein substrates. (frontiersin.org)
- This observation may contribute to explaining how specificity is established in the seemingly promiscuous interactions of BY-kinases with their cellular substrates. (frontiersin.org)
- Deoxyribonucleoside kinases, which catalyse the phosphorylation of deoxyribonucleosides, are present in several copies in most multicellular organisms and therefore represent an excellent model to study gene duplication and specialisation of the duplicated copies through partitioning of substrate specificity. (ruc.dk)
- Dependent on the initial staurosporine scaffold the organoruthenium complexes have provided marked specificity for the GSK3 and PIM kinases by the introduction of the metallic centre coordinated by a cyclopentadienyl ring and a CO ligand. (wallinside.com)
Acceptor3
- Nevertheless, the enzyme's high thermostability and broad acceptor specificity makes it a valuable candidate for industrial disaccharide synthesis. (ugent.be)
- As the size of the ('3)H-oligosaccharide acceptor increases, the maximum velocity of the enzyme increases for chondroitin-6-sulfate and chondroitin substrates. (illinois.edu)
- The contributions of side chains that provide key interactions with the acceptor substrate, defining its specificity, have also been quantitated. (ubc.ca)
Structural5
- Critical issues examined include the function of water molecules in providing strength and specificity of binding, the extent to which binding subsites are interdependent, and the roles of polypeptide chain flexibility and distal structural elements in contributing to specificity profiles. (nih.gov)
- Porcine liver carboxylesterase 1 specificity for amino acid esters of three nucleoside analogs [floxuridine, gemcitabine, and 2-bromo-5,6-dichloro-1-(β- d -ribofuranosyl) benzimidazole] was evaluated to assess optimal structural preferences for prodrug design. (aspetjournals.org)
- The mechanisms of intramembrane proteases are incompletely understood due to the lack of structural data on substrate complexes. (embopress.org)
- Kinetic analyses of mutants of ST3Gal-I, in conjunction with structural studies, have confirmed the mechanistic roles of His302 and His319 as general acid and base catalysts, respectively, and have quantitated other interactions with the cytosine monophosphate-N-acetyl beta-neuraminic acid donor substrate. (ubc.ca)
- Here, we show that the closely related cytochrome c peroxidase enzyme can duplicate the substrate binding properties of ascorbate peroxidase through the introduction of relatively modest structural changes at Tyr36 and Asn184. (le.ac.uk)
Wide range of substrates3
- The enzyme oxidizes a wide range of substrates, and relative reaction rates with partially purified Oxygenase NBZ revealed a preference for 3-nitrotoluene, which was shown to be a growth substrate for JS765. (asm.org)
- In addition, we have extended preliminary studies that showed that NBDO can oxidize a wide range of substrates ( 18 ). (asm.org)
- The betaine-choline-carnitine (BCC) transporter family comprises secondary carriers that facilitate the transport of a wide range of substrates that bear trimethylammonium groups ([‐N + (CH 3 ) 3 ]), such as betaine, choline, l ‐carnitine and γ‐butyrobetaine ( Ziegler et al , 2010 ). (embopress.org)
Nicked substrates that contain1
- It will also efficiently ligate many undesirable structures, including substrates containing gaps of one or more nucleotides and nicked substrates that contain DNA base pair mismatches (12-15). (neb.com)
Synthesis1
- Moreover, a single amino acid substitution enlarged the active-site cavity enough to accommodate the larger farnesyl pyrophosphate substrate and led to the efficient synthesis of sesquiterpenes, while alternate single substitutions of this critical amino acid yielded five additional terpene synthases. (plantcell.org)
Peptides2
- The peptides were pooled, treated with purified microsomal TACE, and the reaction mixtures were passed over a streptavidin affinity column to remove unreacted substrate and the Nterminal biotinylated product. (eurekaselect.com)
- 25 of the substrates were resynthesized as discrete peptides and assayed with recombinant TACE. (eurekaselect.com)
Interactions5
- Studies of the substrate specificity, enzyme-substrate interactions, and the function of lipid. (semanticscholar.org)
- Our results suggest that the respective interactions of SalA and TkmA with PtkA favor phosphorylation of different protein substrates in vivo and in vitro . (frontiersin.org)
- These results were rationalized based on the enzyme-substrate interactions observed in a homology model with a docked ligand. (ugent.be)
- By exploiting the fact that the conformational stabilization of a protein is altered upon ligand binding due to specific interactions, and using an array of selectively chosen ligand analogs, one can quantify the contribution individual interactions have on specificity. (diva-portal.org)
- In contrast, the absence of these stabilizing interactions with type II substrates may result in poor conversion. (caltech.edu)
Bacterial2
- Substrate specificity and redox potential of AhpC, a bacterial peroxiredoxin. (semanticscholar.org)
- Herein, we demonstrate that a bacterial PAL from Anabaena variabilis (AvPAL) displays significantly higher activity towards a series of non-natural substrates than previously described eukaryotic PALs. (manchester.ac.uk)
Kinetic4
- Kinetic analysis reveals that the major source of the substrate specificity lies in changes in K(m) for the various substrates. (nih.gov)
- The substrate specificity was investigated in detail by measuring the relative activity on a range of alternative acceptors, applied in the reverse synthetic reaction, and determination of the kinetic parameters for the best acceptors. (ugent.be)
- Kinetic analysis of OXA-46 revealed a specificity for narrow-spectrum substrates, including oxacillin, other penicillins (but not temocillin), and narrow-spectrum cephalosporins. (asm.org)
- Substrate specificity of Ca(2+)/calmodulin-dependent protein kinase phosphatase: kinetic studies using synthetic phosphopeptides as model substrates. (semanticscholar.org)
Gene4
- The MDR 1 gene product, the adenosine triphosphate (ATP)-binding cassette (ABC) transporter ABCB1 or P-gp, is an ATP-driven efflux pump contributing to the pharmacokinetics of drugs that are P-gp substrates and to the multidrug resistance of cancer cells ( 1 , 2 ). (sciencemag.org)
- We cloned this gene and characterized its specificity to the length of the substrate using heterologous expression in Escheriсhia coli . (springer.com)
- We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. (elifesciences.org)
- Despite the increase in gene copy number, zebrafish aquaporins mostly retain the substrate specificity characteristic of the tetrapod counterparts. (uib.no)
Enzymatic5
- Many important experiments in proteomics including protein digestion, enzyme substrate screening, enzymatic labeling, etc., involve the enzymatic reactions in a complex system where numerous substrates coexists with an enzyme. (mcponline.org)
- In such experiments, an enzyme was incubated with numerous competing substrates for enzymatic reaction which would generate numerous different products. (mcponline.org)
- The state of art high throughput assay approaches like mass spectrometry-based proteomics are able to monitor the changing of substrates or products during the course of this type of complex enzymatic reactions. (mcponline.org)
- Enzymatic properties and substrate sp. (ugent.be)
- Van der Borght J, Chen C, Hoflack L, Van Renterghem L, Desmet T, Soetaert W. Enzymatic properties and substrate specificity of the trehalose phosphorylase from Caldanaerobacter subterraneus. (ugent.be)
Vitro2
- The results described herein are a first step toward the systematic evaluation of a panel of dog P450s and the development of dog P450 isoenzyme-selective marker substrates, as well as providing useful information on prediction and extrapolation of the results from in vitro to in vivo and from dog to human. (aspetjournals.org)
- Thus, both the in vitro and in vivo substrate specificity of Pho85 is determined by the cyclin partner. (asm.org)
Affinity1
- Interestingly, the abrogation of the LeuRS specificity determinant threonine 252 did not improve the affinity of the editing site for the cognate leucine as expected, but instead substantially enhanced the rate of leucyl-tRNA Leu hydrolysis. (elsevier.com)
Mismatch discrimination1
- In doing so, we define the role of induced-fit in nucleotide specificity and mismatch discrimination. (utexas.edu)
Arginine4
- Computer graphic analysis suggested that these substitutions would differentially affect arginine and lysine substrate binding of the enzyme. (nih.gov)
- The novel human protein arginine N-methyltransferase PRMT6 is a nuclear enzyme displaying unique substrate specificity. (semanticscholar.org)
- In most cases the results show flexibility in the P4 position, very high specificity for arginine in the P3 position and glycine in the P2 position, in accord with the sequence of the natural substrate, ubiquitin. (portlandpress.com)
- Moreover, besides the effect of substrate entrance on its own, we strongly suggest that a highly conserved arginine residue (in the RDP motif) rather than the previously proposed Tyr motif (not conserved) provides the proton to increase the pKa of the acid-base catalyst. (kuleuven.be)
Subunit1
- Sin1CRIM fused to a different TORC2 subunit can recruit the TORC2 substrate Gad8 for phosphorylation even in the sin1 null mutant of fission yeast. (elifesciences.org)
High specificity1
- Here we show that RdgB protein and RdgB homologs from Saccharomyces cerevisiae, mouse, and human all possess deoxyribonucleoside triphosphate pyrophosphohydrolase activity and that all four RdgB homologs have high specificity for dHAPTP and deoxyinosine triphosphate compared with the four canonical dNTPs and several other noncanonical (d)NTPs. (nih.gov)
Fluorescent substrates1
- Two independent drug-selected cell line pairs expressing human or mouse ABCG2 were compared for efflux of fluorescent substrates using flow cytometry. (aspetjournals.org)
Assay2
- Here, we present the development of a screening assay for the substrate specificity of para -phenol oxidases based on the detection of hydrogen peroxide using the ferric-xylenol orange complex method. (mdpi.com)
- The assay was used to screen the activity of VAO and EUGO towards a set of twenty-four potential substrates. (mdpi.com)
Amino acids2
- In the present study, site-directed mutagenesis of both native and mutated ADH1 genes was performed in order to identify the key amino acids involved in this substrate shift, resulting in Adh1p-variants with different substrate specificities. (diva-portal.org)
- Overall, the results presented in this work indicate that in addition to the P1 and P1′ positions, additional amino acids within a six-residue window (between P4 and P2′) contribute to the binding of substrate polypeptides to the OmpT binding site. (asm.org)
Proteases1
- Calpains are intracellular Ca(2+)-dependent Cys proteases that play important roles in a wide range of biological phenomena via the limited proteolysis of their substrates. (nih.gov)
Conformational changes1
- The result is a polymerase that is kinetically indistinguishable from the wild-type enzyme, but provides a signal to monitor changes in enzyme structure that result from conformational changes induced by substrate binding. (utexas.edu)
Residue3
- Super-reactive' substrate sequences were engineered, with more than a 2-fold increase in activity, by combining the best residue choices at P5 to P3 positions. (hkmj.org)
- This change in specificity occurs even though residue 262 is remote from the active site. (caltech.edu)
- We investigated the substrate specificities of five other point mutants resulting from single-nucleotide substitutions at positions near residue 262: G262A, G262V, S121G, F218Y, and F218I. (caltech.edu)
Phosphorylation2
- Their function is to regulate different cellular processes via phosphorylation of protein substrates. (frontiersin.org)
- That study had, however, not established whether MinD-dependent activation of PtkA can lead to specific phosphorylation of any of the PtkA substrates. (frontiersin.org)
Sequence1
- The full spectrum of this substrate specificity, however, has not been clarified using standard sequence analysis algorithms, e.g., the position-specific scoring-matrix method. (nih.gov)
Physiological2
- The components of MEN that act upstream of Dbf2-Mob1 have been characterized, but physiological substrates for Dbf2-Mob1 have yet to be identified. (caltech.edu)
- The d-myo-inositol in the physiological substrate was successfully replaced by cyclohexanediol and is still a substrate for T. brucei GlcNAc-PI de-N-acetylase. (lancs.ac.uk)
Preferentially2
- This improved understanding of EaDAcT specificity confirms that the enzyme preferentially utilizes acetyl-CoA to acetylate sn-1,2-DAGs and will be helpful in engineering the production of acetyl-TAG with improved functionality in transgenic plants. (k-state.edu)
- Herein, we demonstrate that the microenvironment from which Ras signals emanate determines which substrates will be preferentially phosphorylated by the activated ERK1/2. (hud.ac.uk)
Assays2
- These oligosaccharides were utilized as substrates in glucuronosyl transferase II assays. (illinois.edu)
- The oligosaccharide substrates were quantitatively reduced and radiolabeled with NaB('3)H(,4) and then purified to homogeneity by high performance liquid chromatography for use in the enzyme assays. (illinois.edu)
Hydrolysis1
- Substrate specificity of glutamyl endopeptidase (GE): hydrolysis studies with a bovine α-casein preparation. (ul.ie)
Probing1
- Probing the substrate specificity of Trypanosom. (lancs.ac.uk)
Single amino acid1
- Alteration of a single amino acid changes the substrate specificity of dihydroflavonol 4-reductase. (semanticscholar.org)