Carbohydrate structural homology protein. Medical search. Frequent questions

Sequence conservation in this family has pointed to a conserved core, termed the NodB homology domain. (rcsb.org)
The PdaA structure provides a template for interpreting the wealth of sequence data on family 4 carbohydrate esterases in a structural context and represents a first step towards understanding the reaction mechanism of this family of enzymes. (rcsb.org)
N, P, M, G and L share significant sequence homology and/or structural characteristics with the homologous proteins of other rhabdoviruses. (ictv.global)
Finally, these new peptides reveal a carbohydrate moiety, indicating a glycosylation in the sequence. (springer.com)
Peptides were characterized by a combined use of MALDI- TOF/TOF and nanoESI-IT-ETD experiments to determine not only the peptide sequence but also the composition and the position of the carbohydrate moiety. (springer.com)
The two domains have high structural homology despite minimal sequence homology. (unl.edu)
basic concepts of sequence alignment: local and global alignments, Needleman and Wunsch, Smith and Waterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of Nucleic acid and protein sequences and interpretation of results Multiple sequence alignments (MSA): the need for MSA, basic concepts of various approaches for MSA (e.g. progressive, hierarchical etc. (entrance.net.in)
Sequence analyses of unigenes revealed four potential groups: hydrolases, cell envelope associated proteins (CEAPs), candidate effectors and other proteins. (biomedcentral.com)
This was gradually expanded into various methods in bioinformatics, in particular for sequence analysis and protein structure prediction. (ntnu.edu)
The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. (concordia.ca)
Here, we present results of a recent search of the protein sequence database for new DS domains using generalized profiles, a sensitive multiple alignment-based search technique. (embl-heidelberg.de)
The proposed alignment with the galactose oxidase sequence makes it possible to construct homology-based three-dimensional models for the most interesting examples, as illustrated by an accompanying paper on the C1 and C2 domains of factor V. (embl-heidelberg.de)
It has been shown to be a bacterial homolog of eukaryotic tubulin, based both on a low sequence identity and a striking structural similarity (2). (cytoskeleton.com)
Most attempts made focus on sequence motifs of protein-protein interactions, binding sites, or sequence conservancy. (biomedcentral.com)

CRP proteins function as cyclic nucleotide-regulated transcription factors that modulate the expression of genes encoding enzymes involved in carbohydrate metabolism. (wikipedia.org)
The sprivivirus genome contains five genes in the order 3′- N - P - M - G - L- 5′ encoding a nucleoprotein, polymerase-associated protein, matrix protein, glycoprotein and RNA-directed RNA polymerase, respectively (Figure 1. (ictv.global)
Eukaryotic expression vectors containing genes encoding plant proteins for killing of cancer cells. (weeksmd.com)
consequently, genes encoding some of these proteins are being used to design constructs for the inhibition of multiplying cancer cells. (weeksmd.com)
Eleven candidate effector genes were identified based on features common to characterized fungal effectors, i.e. they encode small, soluble (lack of transmembrane domain), cysteine-rich proteins with a putative SP. (biomedcentral.com)
Analyzing the diversity of these proteins in vascular plants led to the identification of PP2-like genes in species from 17 angiosperm and gymnosperm genera. (lookformedical.com)
The conserved PP2 domain was identified in the proteins encoded by six genes from several cucurbits, celery (Apium graveolens), and Arabidopsis that are specifically expressed in the sieve element-companion cell complex. (lookformedical.com)
ncRNAs with more than 200 nucleotides are considered as lncRNAs, which originate from intronic and exonic regions of protein-coding genes in both sense and antisense strands, as well as from the intergenic regions [ 21 ]. (biomedcentral.com)
2010) Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate- borne fibrolytic enzymes. (concordia.ca)
This region of DNA homology included the wzx and wzy genes. (microbiologyresearch.org)

In addition to enzymes from hydrolases, transferases and isomerases, it contains also some non-enzymatic proteins involved in amino acid transport. (or.jp)
Finally, it is probable that the specificity of α-amylase is present also in the family GH126, although biochemical evidence is still unclear with regard to the endo- vs. exo-mode of action of the only characterized "amylase" from Clostridium perfringens, which, moreover, exhibits a structural homology with β-glucan-active enzymes employing inverting reaction mechanism. (or.jp)
In addition to GH families reflecting classification based on catalytic domains, the so-called starch-binding domains of amylolytic enzymes classified among more than 10 carbohydrate-binding module (CBM) families, like CBM20, CBM21 and others, has attracted scientific interest, too. (or.jp)
O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases. (toulouse-biotechnology-institute.fr)
2022. Analysis of Carbohydrate-Active Enzymes and Sugar Transporters in Penicillium echinulatum: a Genome-wide Comparative Study of the Fungal Lignocellulolytic System. (openwetware.org)

Peptide bond, phi, psi and chi torsion angles, ramachandran map, anatomy of proteins - Hierarchical organization of protein structure - Primary. (entrance.net.in)
These proteins show similar domain architectures as known organelle-targeted expression regulators of the octotrico peptide repeat type in algae and plants. (frontiersin.org)
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. (bvsalud.org)

Family 4 carbohydrate esterases deacetylate polymeric carbohydrate substrates such as chitin, acetyl xylan and peptidoglycan. (rcsb.org)
Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. (concordia.ca)

The CRD and SCR domains in 13 G3 sequences were each subjected to structural analysis. (brighton.ac.uk)
Thus thousands of protein sequences possessing tens of various amylolytic enzyme specificities from Bacteria, Archaea and Eucarya (some of them still waiting to be discovered) offer a scientific material worth of the in silico studies that subsequently could lead to their protein engineering and design. (or.jp)
DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12. (openwetware.org)

Herein, we report the structural and functional characterization of Mtb-UspC. (warwick.ac.uk)
This study describes the structural characterization of a totally new family of peptides from the venom of the snake green mamba ( Dendroaspis angusticeps) . (springer.com)
The last two features have made the structural characterization of the new peptides by mass spectrometry a real analytical challenge. (springer.com)
Here, we report the identification and characterization of a Tle3 phospholipase effector and its cognate immunity protein Tli3-an outer membrane lipoprotein from adherent-invasive Escherichia coli (AIEC). (bvsalud.org)
In this study, we present the biochemical and immunological characterization of Api g 5, a glycoprotein allergen from celery with homology to FAD containing oxidases. (lookformedical.com)
Characterization of promoters in archaeal genomes based on DNA structural parameters. (openwetware.org)
2012). Structural, biochemical, and functional characterization of the cyclic nucleotide binding homology domain from the mouse EAG1 potassium channel . (up.pt)

Significant structural similarity is evident between the Popeye domain and cAMP binding domains of eukaryotic protein kinase A (PKA) and HCN channels. (wikipedia.org)
Members of the discoidin (DS) domain family, which includes the C1 and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been implicated in cell-adhesion or developmental processes. (embl-heidelberg.de)

Cells of the same strain protect themselves against effectors with immunity proteins that specifically inhibit effectors. (bvsalud.org)
Using potato virus X (PVX) based transient expression assays, we showed that one of the candidate effectors, i. e. contig 8 that encodes a cerato-platanin (CP) domain containing protein, unlike CP proteins from other fungal pathogens was unable to elicit a hypersensitive response (HR). (biomedcentral.com)
I-branched carbohydrates as emerging effectors of malignant progression. (nih.gov)

FtsZ is a bacterial cytoskeletal protein that is essential for cell division many prokaryotes (1). (cytoskeleton.com)

We showed, experimentally, that Tle3AIEC interacts with the VgrG AIEC cargo protein and AlphaFold2 prediction of the VgrGAIEC-Tle3AIEC complex reveals a strong interaction between the VgrGAIEC C-terminus adaptor and Tle3AIEC N-terminal loop. (bvsalud.org)
Structure prediction, Molecular Dyanamics stimulations of endopolygalacturonase and its interaction with PGIP (polygalacturonase-inhibiting protein). (cabgrid.res.in)
The discoidin domain family revisited: new members from prokaryotes and a homology-based fold prediction. (embl-heidelberg.de)

Examples include finding proteins indicating cardiac problems or looking for circulating tumour cells that can indicate the spread of cancer. (50webs.com)

This gene encodes a member of the POP family of proteins which contain three putative transmembrane domains. (wikipedia.org)

A complex with the substrate analogue N-acetyl-glucosamine was refined to 2.25 A resolution, revealing interactions of an aspartic acid and three histidines, all conserved in the NodB homology domain, with the ligand. (rcsb.org)
Homology modelling showed that four of these residues are located on a surface region on the CRD that is separate from the Ca2+-binding residues involved in carbohydrate interactions. (brighton.ac.uk)
To achieve our projects, we purify proteins, and analyze the physical properties and molecular interactions using biophysical methods such as circular dichroism (CD), isothermal titration calorimetry (ITC), and surface plasmon resonance (SPR) biosensor. (kpu-biophyschem.com)
The results can be applied in protein engineering to increase protein stability and function, and further, for rational design of small molecules to inhibit molecular interactions. (kpu-biophyschem.com)
The present targets for protein interactions are as follows. (kpu-biophyschem.com)
We overexpress and purify adaptor proteins, Growth factor receptor bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), phosphatidylinositol-3 kinase (PI3K), and their SH2 domains, and analyze their molecular interactions with the intracellular regions of CD28, ICOS, and CTLA-4. (kpu-biophyschem.com)
Mainly focus on proteins with regard to their structures, functions, mutations and interactions. (cabgrid.res.in)

The cyclic AMP-binding domains of these proteins display approximately 25% identity and 60% similarity to the Popeye domain. (wikipedia.org)

Mtb-UspC (Rv2318) is the solute-binding protein of the essential transporter UspABC, one of four Mtb ABC transporters implicated by homology in sugar acquisition. (warwick.ac.uk)
However, the limited set of chromatophore-encoded solute transporters appears insufficient for supporting metabolic connectivity or protein import. (frontiersin.org)
Here we show by mass spectrometric analyses of enriched insoluble protein fractions that, unexpectedly, nucleus-encoded transporters are not inserted into the chromatophore inner envelope membrane. (frontiersin.org)

1W1B: Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. (rcsb.org)
In serotype 4b, gtcA appears to be the first member of a bicistronic operon which includes a gene with homology to Bacillus subtilis rpmE , encoding ribosomal protein L31. (asm.org)

The 1.5 Å resolution structure of UspC reveals a two subdomain architecture that forms a highly acidic carbohydrate-substrate binding cleft. (warwick.ac.uk)

For carbohydrate transport and metabolism, trehalose synthase is required. (sciforum.net)
The NPC1 protein is involved in the intracellular lipid metabolism coordinating sterol trafficking. (biomedcentral.com)

There are also five conserved basic residues in the G3 SCR that are atypical of the SCR superfamily, and homology modelling showed that all five were located on one surface of the SCR. (brighton.ac.uk)
Diversity of the superfamily of phloem lectins (phloem protein 2) in angiosperms. (lookformedical.com)
Within this superfamily, PP2 proteins have considerable size polymorphism. (lookformedical.com)

Kumar S*, Behera SK, Gururaj K, Chaurasia A, Murmu S, Prabha R, Angadi UB, Pawaiya RS, Rai A (2023) In silico mutation of aromatic with aliphatic amino acid residues in Clostridium perfringens epsilon toxin (ETX) reduces its binding efficiency to Caprine Myelin and lymphocyte (MAL) protein receptors. (cabgrid.res.in)

High-resolution 3D structures of type 2 secretion system (T2SS) secretins revealed bimodular channels with a C-module, holding a conserved central gate and an optional top gate, followed by an N-module for which multiple structural organizations have been proposed. (bvsalud.org)
Carbohydrate analysis of the allergen revealed the presence of glycans carrying fucosyl and xylosyl residues, structures previously shown to bind IgE. (lookformedical.com)
We analyze 3D structures and structural dynamics at atomic resolution using X-ray crystallography and nuclear magnetic resonance (NMR). (kpu-biophyschem.com)
We propose a graph-theory approach with significance and power testing to identify modules in protein structures. (biomedcentral.com)
This modularity gives protein structures enhanced flexibility [ 3 ] and might influence its ability to respond to selection. (biomedcentral.com)

The enzyme assumes a fold related to a (beta/alpha)8 barrel, with a long groove on the surface of the protein that harbours all conserved residues. (rcsb.org)
The encoded protein is the I-branching enzyme, a beta-1,6-N-acetylglucosaminyltransferase responsible for the conversion of fetal i antigen to adult I antigen in erythrocytes during embryonic development. (nih.gov)

Carbohydrate Polymers, 132 , 378 - 396. (up.pt)
Carbohydrate Polymers, 90 (1), 270 - 274. (up.pt)

We were able to describe functional/structural sub-domain architecture related to key residues for starch cleavage, calcium, and chloride binding sites in the α -amylase, and sterol opening-defining modules and disease-related residues in the NPC1. (biomedcentral.com)

Three S. enterica isolates had O antigen gene clusters with homology to the Escherichia coli O123 O antigen region. (microbiologyresearch.org)

Popeye domain-containing protein 2 is a protein that in humans is encoded by the POPDC2 gene. (wikipedia.org)
Popeye domain containing proteins are essential for stress-mediated modulation of cardiac pacemaking in mice" (PDF). (wikipedia.org)
G3 is implicated in the intracellular processing of aggrecan and contains a C-type lectin carbohydrate recognition domain (CRD), frequent occurrences of a C-terminal short complement repeat (SCR) domain, and occasionally an N-terminal epidermal growth factor domain. (brighton.ac.uk)
One conserved basic residue is identical in position with that of a conserved basic residue that mediates hyaluronate binding in the structurally related proteoglycan tandem repeat (PTR) domain in G1 and in link protein. (brighton.ac.uk)
The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. (embl.de)
Taxonomic distribution of proteins containing TSP1 domain. (embl.de)
The complete taxonomic breakdown of all proteins with TSP1 domain is also avaliable . (embl.de)
Click on the protein counts, or double click on taxonomic names to display all proteins containing TSP1 domain in the selected taxonomic class. (embl.de)
Endo-1,3-β-glucanase from Cellulosimicrobium cellulans is composed of a catalytic domain and a carbohydrate-binding module. (kpu-biophyschem.com)
Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes. (embl-heidelberg.de)
In the Dictyostelium discoideum (Slime mold) cell adhesion protein discoidin, a related domain, named discoidin I-like domain, DLD, or DS, has been found which shares a common C-terminal region of about 110 amino acids with the FA58C domain, but whose N-terminal 40 amino acids are much less conserved. (embl-heidelberg.de)
More importantly, we present statistical, structural, and functional evidence that the D1 domain of galactose oxidase whose three-dimensional structure has been determined at 1.7 A resolution, is a distant member of this family. (embl-heidelberg.de)
We also analyzed the evolutionary modularity of a data set of α -amylase catalytic domain homologs, and the dynamic modularity of the Niemann-Pick C1 (NPC1) protein N-terminal domain. (biomedcentral.com)

the phosphorylated protein binds up to 100-fold more calcium than the dephosphorylated protein. (lookformedical.com)

The bacterial CAP or CRP proteins are the closest related non-Popdcproteins. (wikipedia.org)
Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)

Two critical factors during this dauntingly complex process appear to be the establishment of metabolic connectivity between the symbiotic partners, and the evolution of nuclear control over protein expression levels within the organelle. (frontiersin.org)

We overexpress and purify the respective domains and their mutants, and analyze the catalytic function and the carbohydrate recognition mechanism. (kpu-biophyschem.com)
In addition, we also design mutants to modulate catalytic function and carbohydrate binding. (kpu-biophyschem.com)

The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. (unl.edu)
It also leads to a qualitative explanation for the thermodynamic data on sugar-binding to the lectin, with special emphasis on the role of a tyrosyl residue in the variable loop in the sugar-binding region in generating the carbohydrate specificity of WBAII. (unboundmedicine.com)

An understanding of both the genetic and structural composition of Salmonella and E. coli O antigens is necessary for the development of novel molecular methods for serotyping these organisms. (microbiologyresearch.org)
Furthermore, chromatophore-localized biosynthetic pathways as well as multiprotein complexes include proteins of dual genetic origin, suggesting that mechanisms evolved that coordinate gene expression levels between chromatophore and nucleus. (frontiersin.org)

Nearly 39% of the ESTs were predicted to encode proteins of fungal origin and among these, 162 ESTs were predicted to contain N-terminal signal peptides (SPs) in their deduced open reading frames (ORFs). (biomedcentral.com)

We overexpress and purify single-chain Fv (scFv) antibodies, and analyze the structural dynamics and the antigen recognition mechanism. (kpu-biophyschem.com)

Previous studies have demonstrated that lncRNAs act as one of the molecular mechanisms for the post-transcriptional regulation and modulation of protein function. (biomedcentral.com)

TY - JOUR T1 - Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin. (unboundmedicine.com)

Both flagellar and somatic (mostly carbohydrate) surface antigens contribute to the serotypic designation of the organism ( 36 ). (asm.org)

This membrane associated protein is predominantly expressed in skeletal and cardiac muscle. (wikipedia.org)
A vacuole membrane-associated calcium-binding protein with an apparent mass of 45 kD was purified from celery (Apium graveolens). (lookformedical.com)

2016). Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium . (up.pt)

C. truncatum likely secretes an arsenal of proteins that are implicated in maintaining a compatible interaction with its host. (biomedcentral.com)
Some of these proteins may have a role in establishing compatible interaction with the host plant. (biomedcentral.com)
During the transition, C. truncatum probably secretes a range of proteins to establish a compatible interaction with its host, including some that may exclusively be involved in switching the pathogen to the necrotrophic phase. (biomedcentral.com)

Using molecular techniques to differentiate M protein classes, Bessen et al. (cdc.gov)
IgE inhibition immunoblots showed that native Api g 5 other than the deglycosylated protein completely inhibited IgE binding to high molecular weight allergens in protein extracts from birch pollen, mugwort pollen, and celery. (lookformedical.com)

The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. (unl.edu)
a remote homology of clan GH-H to family GH31 containing functionally related α-glucosidases being also already suggested. (or.jp)
Furthermore, our mass spectrometric analysis revealed an expanded family of chromatophore-targeted helical repeat proteins. (frontiersin.org)

GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. (unl.edu)
In this research, an in silico approach was therefore formulated for functional and structural documentation of the uncharacterized protein NCGM946K2 146.Three distinct servers, including Modeller, Phyre2, and Swiss Model were used to evaluate the predicted tertiary structure. (sciforum.net)

Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. (lookformedical.com)

recognized 2 M protein-related antigenic groups (I and II) in GAS that matched known skin and throat M serotypes ( 7 ). (cdc.gov)

The top materials are selected using structural evaluations conducted with the analysis of Ramachandran Plot, Swiss-Model Interactive Workplace, Prosa-web, Verify 3D, and Z scores. (sciforum.net)
This analysis aimed to uncover the value of the NCGM946K2 146 protein of MTB. (sciforum.net)
Crystal structural analysis so far indicates that Cut190 fluctuates in solution and the specific conformers are increased upon Ca 2+ binding. (kpu-biophyschem.com)

This protein, VCaB45, is enriched in highly vacuolate tissues and is located within the lumen of vacuoles. (lookformedical.com)

PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). (bvsalud.org)

This research will, therefore, improve our pathogenesis awareness and give us a chance to target the protein compound. (sciforum.net)

There are 144158 TSP1 domains in 35805 proteins in SMART's nrdb database. (embl.de)
The acquisition of additional modular domains in the amino-terminal extensions of other PP2-like proteins could reflect divergence from its phloem function. (lookformedical.com)
There are 23298 FA58C domains in 16898 proteins in SMART's nrdb database. (embl-heidelberg.de)
We still use a similar thought relating protein evolution, since domains are accepted as the protein evolutionary modules, and its modular reuse has been demonstrated in all domains of life [ 2 ]. (biomedcentral.com)

Given the limited availability of carbohydrates within the phagosomal environmental niche during Mtb intracellular infection, our studies suggest that UspABC enables Mtb to optimize the use of scarce nutrients during intracellular infection, linking essentiality of this protein to a potential role in recycling components of cell-wall peptidoglycan. (warwick.ac.uk)

My research interests are related to understanding the correlation between protein structure and function. (kpu-biophyschem.com)
We specifically focus on the protein flexibility, which is difficult to determine but is critical for understanding protein structure-function relationship. (kpu-biophyschem.com)
In the protein world, the phenotype is the structure and the phenotypic variance is given by slight variations in protein structure shape. (biomedcentral.com)

One of the interacting proteins is the two-pore potassium (K2P) channel TREK-1. (wikipedia.org)

The N-linked carbohydrate of properdin is not required for oligomerization or stabilization of the C3b-Bb complex. (embl.de)

GCS/GGS only possesses class I M protein with a surface-exposed conserved region similar to M protein of known rheumatogenic GAS strains ( 4 ). (cdc.gov)

Anatomy3

Organisms5

Chemicals and Drugs35

Analytical, Diagnostic and Therapeutic Techniques and Equipment15

Phenomena and Processes40

Disciplines and Occupations1

Technology, Industry, Agriculture2

Information Science5

Sequence14

Genes10

Enzymes5

Peptide3

Esterases2

Sequences3

Characterization7

Eukaryotic2

Effectors3

Cytoskeletal protein1

Prediction3

Include finding1

Putative1

Interactions7

Cyclic1

Transporters3

Bacillus2

Cleft1

Metabolism2

Superfamily3

Amino acid1

Structures5

Enzyme2

Polymers2

Residues1

Clusters1

Domain13

Binds1

Bacterial2

Metabolic1

Catalytic2

Residue2

Genetic2

Peptides1

Antibodies1

Mechanisms1

Acidic1

Antigens1

Membrane associated2

Mutations1

Interaction3

Molecular2

Family3

Distinct2

Abundant1

Antigenic1

Analysis3

Lumen1

Quaternary1

Compound1

Domains4

Intracellular1

Structure3

Potassium1

Stabilization1

Strains1