ResiduesProteinAcidsHistidineAlanineProteinsMechanismSubstrateSerineBiosyntheticResidueTriadMetabolismDegradationCellularDehydrogenaseEnzymeSubunitGABAPutativeCleftFree aminoMethionineCysteineActivityPathwayEnzymesMetal ionsCofactorLigandsInterproscanIdentificationWeaklyProlinePhosphateKinaseCavityAffinityDomainMolecularProcessEncodes
Residues7
- This triad of residues includes a nucleophilic cysteine, a glutamate base, and a lysine, all of which are conserved within the structure. (wikipedia.org)
- With the conserved Zn(2+)-binding motifs HEXXH and NEXFA as well as the N-terminal substrate-anchoring glutamate residues, F3 together with the leukotriene A4 hydrolase, represents a novel gluzincin subfamily of aminoproteases. (rcsb.org)
- In the ACE2 receptor, the largest number of amino acids playing a crucial role in the mechanism of interaction and recognition with the S protein is located in the C-terminal part, which represents the main binding region between ACE2 and S. This fragment is abundant in coordination residues such as aspartates, glutamates, and histidine that could be targeted by metal ions. (bvsalud.org)
- In catalytic triades as a negatively charged counterpart, on the surface of proteins as an exposed polar residue, in salt bridges along with cationic residues when these are not exposed to the solvent, in coordination of some metal ions, in binding pockets for accommodation of positively charged substrates. (chemsynbio.com)
- In methionine synthase the cobalamin cofactor is sandwiched between the B12-binding domain and an ~90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices [ 4 ]. (expasy.org)
- These residues are between 6.1-6.7Å apart, which is consistent with a [[retaining]] catalytic mechanism. (cazypedia.org)
- The presence of interactions between the calcium ion and four?glutamate residues in VPI-5482 genomic DNA using primers Rabbit Polyclonal to C56D2 that gave ligation-independent cloning (LIC) compatible ends. (acusticavisual.net)
Protein29
- SARS-CoV-2 infects cells via its spike (S) protein binding to its surface receptor angiotensin-converting enzyme 2 (ACE2) and results in the production of multiple proinflammatory cytokines, especially in the lungs, leading to what is known as COVID-19. (bvsalud.org)
- In this study, we used human cultured mast cells that are plentiful in the lungs and showed that recombinant SARS-CoV-2 full-length S protein (1-10 ng/mL), but not its receptor-binding domain (RBD), stimulates the secretion of the proinflammatory cytokine interleukin-1ß (IL-1ß) as well as the proteolytic enzymes chymase and tryptase. (bvsalud.org)
- The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection relies on its spike protein binding to angiotensin-converting enzyme 2 (ACE2) on host cells to initiate cellular entry. (bvsalud.org)
- The spike protein (S) of SARS-CoV-2 is able to bind to the human angiotensin-converting enzyme 2 (ACE2) receptor with a much higher affinity compared to other coronaviruses. (bvsalud.org)
- The binding interface between the ACE2 receptor and the spike protein plays a critical role in the entry mechanism of the SARS-CoV-2 virus. (bvsalud.org)
- There are specific amino acids involved in the interaction between the S protein and the ACE2 receptor. (bvsalud.org)
- Zn2+ ions bind to the ACE2 receptor in its catalytic site and modulate its activity, but it could also contribute to the structural stability of the entire protein. (bvsalud.org)
- The ability of the human ACE2 receptor to coordinate metal ions, such as Zn2+, in the same region where it binds to the S protein could have a crucial impact on the mechanism of recognition and interaction of ACE2-S, with consequences on their binding affinity that deserve to be investigated. (bvsalud.org)
- encodes a glycine-rich RNA binding protein. (or.jp)
- We also demonstrated that altering the intermediate amino acid did not alter the specificity of the regulatory proteins for their protein substrates. (scirp.org)
- protein_coding" "AAC73194","ftsL","Escherichia coli","membrane bound cell division leucine zipper septum protein [Ensembl]. (ntu.edu.sg)
- protein_coding" "AAC73196","murE","Escherichia coli","UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-diaminopimelate ligase [Ensembl]. (ntu.edu.sg)
- This competitive enzyme-linked immunosorbent assay-like method, used competitive binding of free hyaluronan in the sample and biotin-labeled standard hyaluronan to hyaluronan binding protein in solid phase. (go.jp)
- Allosterically regulated enzymes additionally rely on the free energy of ligand binding to stabilize the protein in a catalytically competent state. (ward-lab.ch)
- We demonstrate the interplay of protein folding energetics and functional group tuning to convert calmodulin (CaM), a regulatory binding protein, into AlleyCat, an allosterically controlled eliminase. (ward-lab.ch)
- 47904) TATA-box binding family protein CP001857 CDS Arcpr_0059 47991. (go.jp)
- A Rab protein is always bound to another molecule, which determines whether it is inactive or active. (elifesciences.org)
- Binding to a molecule called GDP makes the Rab protein inactive, while binding to GTP makes it active. (elifesciences.org)
- Proteins called guanine nucleotide exchange factors, or GEFs for short, activate the Rab protein by promoting the release of GDP and the binding of GTP. (elifesciences.org)
- The experiments showed that different amino acids in the active site of the Rab protein are involved when the GEFs mediate the release of the GDP during the activation process. (elifesciences.org)
- For example, the amino acid glutamine is involved when the Listeria GEF and one of the human GEFs activate the protein, whereas a different amino acid-aspartate-is involved when one of the other human GEFs is responsible for the activation. (elifesciences.org)
- It is a membrane-bound protein that acts as a dimer of two identical subunits. (rcsb.org)
- This diploma thesis revolves around the preparation of biocompatible polymeric conjugates called "iBodies" that will be used to induce targeted lysosomal degradation of two model enzymes - Fibroblast activation protein α, and Glutamate carboxypeptidase II. (nusl.cz)
- You see here the bridging carboxylate group into protein and you have some rough ideas where the oxygen could bind and be reduced. (lindau-nobel.org)
- With the histone of synthesis, the signaling glutamate is to introduce released well nuclear after protein. (evakoch.com)
- Manganese binds to the prion protein, altering its conformation, displacing copper, and altering the redox chemistry of the metal-protein complex. (selfdecode.com)
- It is also believed that this direct disruption of the catalytic [4Fe-4S] cluster of aconitase by manganese produces iron regulary protein 1, resulting in alterations in cellular iron homeostasis. (selfdecode.com)
- This may occur by manganese competing directly for an iron-binding site on the iron binding protein, disrupting the cellular mechanisms responsible for its iron-dependent degradation. (selfdecode.com)
- Lead also binds to metallothionein, a sulfhydryl-rich protein, but does not appear to displace cadmium or zinc. (cdc.gov)
Acids11
- Omega amidase catalyzes the deamidation of several different alpha-keto acids into ammonia and metabolically useful carboxylic acids The general mechanism is the same as for other nitrilases: binding of the substrate to the active site, followed by release of ammonia, formation of a thioester intermediate at the cysteine, binding of water and then release of the carboxylic acid product. (wikipedia.org)
- By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. (frontiersin.org)
- Mutational analysis of several of these amino acids both in pUL105 and pUL70, proved that they are crucial for viral replication. (frontiersin.org)
- We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis. (frontiersin.org)
- It is involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. (expasy.org)
- The fact that the detailed structure of this domain (at the level of individual amino acids) has been conserved over evolution is often taken as an indication that its mechanism has also been conserved. (elifesciences.org)
- It is found on the surface of cells throughout the body where it plays several roles: it interacts with many other proteins, playing important roles in processes such as cell signaling and inflammation, and it inactivates several different hormones, including incretins, by clipping off two amino acids from their ends. (rcsb.org)
- The cleavage reaction is performed by a catalytic triad of amino acids very similar to serine proteases such as trypsin and elastase . (rcsb.org)
- A serine performs the cleavage reaction, which is made more chemically active by nearby histidine and aspartate amino acids. (rcsb.org)
- In the four substrates shown here, the two amino acids at the end, colored blue or green, will be clipped off and released as a dipeptide. (rcsb.org)
- In the present work, we substituted these and nearby amino acids by others expected to affect the efficiency of the enzyme. (inra.fr)
Histidine8
- In plants the regulatory mechanism involves phosphorylation of a threonine residue that is separated by a single amino acid from the histidine residue that forms a phosphorylated intermediate during catalysis. (scirp.org)
- Using antibodies, we demonstrated that the regulation of both Listeria monocytogenes PPDK and Escherichia coli PEP synthetase involves the phosphorylation of a threonine residue located close to the catalytic histidine residue. (scirp.org)
- The amino acid located between the regulatory threonine and the catalytic histidine is highly conserved being serine in PPDK and cysteine in PEPS. (scirp.org)
- A comparison of known PPDK and PEPS sequences revealed a high level of conservation of the amino acid sequence surrounding the catalytic histidine located within a central domain of the enzymes that was composed of GGXTS/CHAAI/VI/VA/SR with the regulatory threonine and catalytic histidine (shown in bold) conserved in all species. (scirp.org)
- In both types of enzymes the B12-binding domain uses an histidine to bind the cobalt atom of cobalamin cofactors. (expasy.org)
- When bound to the B12-binding domain dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. (expasy.org)
- The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles [ 5 ]. (expasy.org)
- Changing G137 to glutamate or histidine was less effective than aspartate in improving OP hydrolase activity and like G137D, it diminished MCE activity, primarily through increases in Km. (inra.fr)
Alanine1
- This enzyme participates in glutamate metabolism and alanine and aspartate metabolism. (wikipedia.org)
Proteins8
- Upon binding to genomic lesions, these enzymes utilise NAD+ to modify a plethora of proteins with mono- and poly(ADP-ribose) signals that are important for subsequent chromatin decompaction and repair factor recruitment3,4. (diamond.ac.uk)
- It should be pointed out that although the two proteins (PPDK and PEPS) share some homology, especially around a central catalytic site, they can be identified using the signature sequences identified by Tjaden and colleagues [10]. (scirp.org)
- What is the function of glutamate in proteins? (chemsynbio.com)
- The Rab subfamily of proteins is part of the large Ras superfamily, and all members of this superfamily are activated and inactivated in a similar way, with the binding and unbinding of GDP and GTP taking place at a structure called the G-domain. (elifesciences.org)
- Each contains two domains: the domains at the top of each subunit are involved in interacting with other extracellular proteins, and the domains at the bottom carry the catalytic triad. (rcsb.org)
- That's the Max Planck Institute of Biophysics in Frankfurt, and we focus on membrane proteins, membrane-bound proteins, which have a number of many different functions. (lindau-nobel.org)
- The ionizable amino acid side chains of proteins are usually located at the surface. (lu.se)
- In the interaction with proteins, lead binds with virtually every available functional group, including sulfhydryl, amine, phosphate, and carboxyl groups, with sulfhydryl having the highest affinity. (cdc.gov)
Mechanism9
- We discuss the functional implications of these structures with respect to the underlying catalytic mechanism, substrate recognition and processing, and possible component interactions. (rcsb.org)
- Kinetic modeling of steady state initial velocity data was consistent with a novel hybrid branching kinetic mechanism which included dissociation of PMP after the first half reaction to generate the apoenzyme which could bind PLP for another catalytic deamination event. (unipr.it)
- The geometry of the active site (three classes have been described), the possible electron donors in vivo and the current hypothesis for the catalytic mechanism will be discussed. (unl.pt)
- Taken together, these findings suggest that the structural strain imposed by ferrochelatase on the porphyrin substrate as a critical step in the enzyme catalytic mechanism is also accomplished by the E287A and E287Q variants, but without the release of the product. (unl.pt)
- FR-binding capacities (a determinant of cellular uptake by this mechanism) and FR RFC and PCFT uptake characteristics for all these CHO cell lines are documented.24 37 For these experiments cells were cultured over a range of drug concentrations and proliferation was measured after 96 h with a fluorescence-based metabolic Amonafide (AS1413) assay (Cell Titer Blue). (crispr-reagents.com)
- Our rational design based the catalytic mechanism of the α -glucosidase reaction proved to be effective for producing mutants with improved the ratio of transglycosylation/hydrolysis of α -glucosidase, which provides an important theoretical basis for further research on the reaction mechanism of α -glucosidase. (researchsquare.com)
- A feature of almost all classical CAZy families is that, since sequence dictates structure, and structure determines function, the catalytic mechanism is conserved within a sequence-based family (Henrissat and Davies, 1997). (acusticavisual.net)
- 2004), and GH23 is a family with both inverting and retaining hexosaminidases, but the catalytic mechanism of neither is understood, and may involve substrate Osthole participation in catalysis. (acusticavisual.net)
- 2003) of this Carbohydrate Active enZymes (CAZy) classification (http://www.cazy.org/), the catalytic mechanism of which was unknown prior to this work, but had been predicted to be retaining in an insightful bioinformatics analysis (Naumoff, 2005). (acusticavisual.net)
Substrate4
- In addition to the catalytic triad, omega-amidase also contains a second glutamate that assists in substrate positioning. (wikipedia.org)
- Specifically, the active site cysteine acts as a nucleophile and binds to the substrate. (wikipedia.org)
- The dehydration of the carboxylate, although intrinsically thermodynamically unfavorable, is achieved by harnessing the free energy of folding and substrate binding to reach the required basicity. (ward-lab.ch)
- Significantly, rapid stopped-flow experiments of the E287A and E287Q Variants demonstrate that reaction with Zn2+ results in the formation of bound Zn-protoporphyrin IX, indicating that the endogenously bound protoporphyrin IX can be used as a substrate. (unl.pt)
Serine1
- C-terminally adjacent to the HID follows a proline, glutamate, serine, and threonine (PEST)-rich domain, mediating proteasomal degradation of these kinases. (nature.com)
Biosynthetic1
- His main research topics have been the design, synthesis, and study of the binding modes of peptidoglycan biosynthetic pathway inhibitors. (degruyter.com)
Residue2
- Remarkably, a single mutation of an apolar residue at the bottom of an otherwise hydrophobic cavity confers catalytic activity on calmodulin. (ward-lab.ch)
- Glutamate-287 (E287) of murine mature ferrochelatase is a conserved residue in all known sequences of ferrochelatase, is present at the active site of the enzyme, as inferred from the Bacillus subtilis ferrochelatase three-dimensional structure, and is critical for enzyme activity. (unl.pt)
Triad2
- Just as omega-amidase shares a general structure organization as other nitrilases, omega-amidase also contains the same catalytic triad within the active site. (wikipedia.org)
- The catalytic triad glutamate transfers a proton to the amide group to create and release ammonia. (wikipedia.org)
Metabolism4
- Amino acid metabolism.biosynthesis.glutamate. (ntu.edu.sg)
- Correlation analysis showed that DOX-induced HF mainly affected phenylalanine, tyrosine, and tryptophan biosynthesis, D-glutamine and D-glutamate metabolism, phenylalanine metabolism, biosynthesis of unsaturated fatty acids, and other metabolic pathways, suggesting abnormal amino acid metabolism, fatty acid metabolism, and glycerol phospholipid metabolism. (frontiersin.org)
- Mn(II) has been shown to inhibit mitochondrial aconitase activity to a significant level, altering amino acid metabolism and cellular iron homeostasis. (selfdecode.com)
- Manganese interferes with amino acid metabolism by inhibiting aconitase, resulting in an increase in citrate levels. (selfdecode.com)
Degradation1
- The physiological effects of ROS include amino acid chain cleavage, DNA degradation and lipid oxidation, among others. (unl.pt)
Cellular1
- Thus, glutamate is a cellular equivalent of an amino group. (chemsynbio.com)
Dehydrogenase2
- Semialdehyde dehydrogenase, NAD-binding [Interproscan]. (ntu.edu.sg)
- A new sensitive assay used to quantitate FXIII activity is based on monitoring the amount of ammonia (NH 3 ) released by using glutamate dehydrogenase and nicotinamide adenine dinucleotide phosphate during the transamidation reaction (cross-linking) by FXIII. (medscape.com)
Enzyme2
- It catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. (expasy.org)
- The reaction starts with the fully reduced form of the enzyme, presumably with a water molecule weakly coordinated to the type-2 copper (Cu-T2) ion and no bridging moiety between the two type-3 copper (Cu-T3) ions.17,22 The incoming di- oxygen is immediately reduced, yielding a peroxide-level intermediate (PI),12 with a peroxide ion bound in the centre of the TNC. (lu.se)
Subunit2
- Here, we tested the hypothesis that wild-type p53 is a negative transcriptional regulator of SLC7A11, the gene encoding the System xc-(SXC) catalytic subunit, xCT, in GBM. (emory.edu)
- The crystal structure of the S. cerevisiae c-subunit ring with bound oligomycin revealed the inhibitor docked on the outer face of the proton-binding sites, deep in the transmembrane region ( Zhou and Faraldo-Gómez 2018 ). (tcdb.org)
GABA1
- In addition to dopamine, manganese is thought to perturbations other neurotransmitters, such as GABA and glutamate. (selfdecode.com)
Putative1
- Cornish and co-workers could show that amino-acid substitutions along the putative PT pathway dramatically decreased the catalytic activities. (nature.com)
Cleft2
- Both substances bind within the folate binding cleft of FR(PDB: 4LRH). (crispr-reagents.com)
- Mutations at other sites near the bottom of the catalytic cleft generally diminished OP hydrolase and MCE activities but one, F309L, also yielded some improvements in OP hydrolase activities. (inra.fr)
Free amino1
- Two acidic glutamates assist with the reaction by holding tightly to the free amino end of the hormone, locking it into position. (rcsb.org)
Methionine1
- The second one is directed against the helical bundle found N-terminal to the B12-binding domain of methionine synthase. (expasy.org)
Cysteine1
- The remaining thioester intermediate is stabilized by the lysine and the backbone amino group following the cysteine. (wikipedia.org)
Activity3
- This second glutamate is why omega-amidase has no activity with glutamine or asparagine, even though they are sized similarly to typical substrates. (wikipedia.org)
- GabT1 from Ppo exhibits a specific activity of 4.9 nmol/min/mg at 30 C (pH 7.5), a somewhat promiscuous amino donor selectivity, and curvilinear steady-state kinetics that do not reflect the predicted ping pong behavior typical of aminotransferases. (unipr.it)
- In its binding with sulfhydryl groups, lead may interfere with the activity of zinc metalloenzymes, as zinc binds to a sulfhydryl group at the active site. (cdc.gov)
Pathway1
- The unmatched catalytic turnover rates of [FeFe]-hydrogenases require an exceptionally efficient proton-transfer (PT) pathway to shuttle protons as substrates or products between bulk water and catalytic center. (nature.com)
Enzymes5
- The derived amino acid sequence of Ov-phy-1 encoded a peptide that was most similar to the two Caenorhabditis elegans prolyl 4-hydroxylase homologues and to the isoform II enzymes of vertebrates. (embl.de)
- The B12-binding domain is mainly found in two families of enzymes present in animals and prokaryotes, which use vitamin B12 (cobalamin) as cofactor. (expasy.org)
- The enzymes that bind methylcobalamin carry out methyl transfer reactions. (expasy.org)
- These enzymes are classified into glycoside hydrolase (GH) families and belong to some of the following families: GH5, GH8, GH10, GH11, GH30 and GH141, according to amino-acid sequence similarities (Verma 2021 ). (springeropen.com)
- 1997). Carbohydrate active enzymes have been classified into families based upon their amino acid sequence similarities (Coutinho and Henrissat, 1999). (acusticavisual.net)
Metal ions2
- For each of these two groups of metal ions, general chemical considerations and the basic principles involved in their toxicity are briefly considered, as well as how the metal ion is bound within cells or tissues, since this is a key element in devising strategies for its removal by chelation. (rsc.org)
- The two essential alkali metal ions Na + and K + (together with H + and Cl − ) are only weakly bound to organic ligands and are extremely mobile. (rsc.org)
Cofactor1
- The B12-binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group or to 5'-deoxyadenosine. (expasy.org)
Ligands1
- That is, the greater the number of NO ligands bound to [2Fe2S], the larger the antiferromagnetic coupling constant. (bvsalud.org)
Interproscan2
- tRNA synthetases class I (I, Anticodon-binding domain of tRNA, Zinc finger found in FPG and IleRS [Interproscan]. (ntu.edu.sg)
- Amino acid kinase family [Interproscan]. (ntu.edu.sg)
Identification1
- Identification and quantification of the porphyrin bound to the E287-directed variants indicate that approx. (unl.pt)
Weakly1
- For example, the carboxylates of glutamate and aspartate are weakly basic in water but become strongly basic when dehydrated in enzymatic sites. (ward-lab.ch)
Proline1
- Proline can be synthesized starting from glutamate. (chemsynbio.com)
Phosphate1
- Analysis of the first half reaction with L-glutamate in the absence of the acceptor fructose 6-phosphate revealed it was capable of catalyzing multiple turnovers of glutamate. (unipr.it)
Kinase1
- We determined the crystal structures of HIPK3 and DYRK1A bound to abemaciclib, showing a similar binding mode to the hinge region of the kinase as observed for Cdk6. (nature.com)
Cavity1
- The catalytic step that initiates formation of the ferric oxy-hydroxide mineral core in the central cavity of H-type ferritin involves rapid oxidation of ferrous ion by molecular oxygen (ferroxidase reaction) at a binuclear site (ferroxidase site) found in each of the 24 subunits. (unl.pt)
Affinity1
- The humanized h357 IgG(1) was then stably expressed in a mammalian cell line and the purified antibody maintained the high antigen binding affinity as compared with the parental m357 based on a soluble TNF-α neutralization bioassay. (bvsalud.org)
Domain4
- In accordance with the close relationship between HIPKs and other DYRK subfamily members, DYRK1A, a class I DYRK member, shares a sequence identity with HIPK3 of 38% within the catalytic domain. (nature.com)
- We report here on peptide amphiphile supramolecular nanofibers that display a sequence from ACE2 in order to promote interactions with the SARS-CoV-2 spike receptor binding domain. (bvsalud.org)
- The first profile recognizes the whole B12-binding domain. (expasy.org)
- Therefore, to evade problems with the missing backbone in the course of this task, the structure was truncated to contain only the C-terminal, catalytic domain, Glyco_hydro_20. (tu-muenchen.de)
Molecular3
- Therefore the molecular docking research expected that 5 and 7 keep key interactions within the binding wallets of FR(Shape 4). (crispr-reagents.com)
- Using chromatin immunoprecipitation studies, we present a molecular interaction whereby p53 binds to the SLC7A11 promoter, suppressing gene expression in PDX GBM cells. (emory.edu)
- These findings suggest that p53 is a molecular switch for GBM glutamate biology, with potential therapeutic utility. (emory.edu)
Process1
- Thus E287 in murine ferrochelatase appears to be critical For the catalytic process by controlling the release of the product. (unl.pt)
Encodes1
- Encodes one of two isoforms of glutamate decarboxylase. (or.jp)