Protein Family Models

Repeat domain from surface fibrillar adhesin CshA. This domain forms several tandem repeats with high sequence identity. CshA is found primarily in streptococci species, but also in other Gram+ bacteria. [1]. 27920201. The Streptococcus gordonii Adhesin CshA Protein Binds Host. Fibronectin via a Catch-Clamp Mechanism.. Back CR, Sztukowska MN, Till M, Lamont RJ, Jenkinson HF, Nobbs. AH, Race PR;. J Biol Chem. 2017;292:1538-1549. (from Pfam)

Date:

2024-08-14

Ths presumed domain is found in the CshA protein from Streptococcus gordonii. The domain is named after the sequence found in CshA in the conserved C-terminal region. The conserved negatively charged residues suggests that this domain may bind to calcium ions. This domain is part of the non-repetitive region NR3 [1]. [1]. 27920201. The Streptococcus gordonii Adhesin CshA Protein Binds Host. Fibronectin via a Catch-Clamp Mechanism.. Back CR, Sztukowska MN, Till M, Lamont RJ, Jenkinson HF, Nobbs. AH, Race PR;. J Biol Chem. 2017;292:1538-1549. (from Pfam)

Date:

2024-08-14

This is the C-terminal domain of Neuron-derived Neurotrophic Factor (NDNF). NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth of hippocampal neurons. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularization. This domain contains the second fibronectin type III domain (FnIII) present in NDNF and one of the two potential consensus sites for N-linked glycosylation [1,2]. [1]. 24706764. Neuron-derived neurotrophic factor functions as a novel. modulator that enhances endothelial cell function and. revascularization processes.. Ohashi K, Enomoto T, Joki Y, Shibata R, Ogura Y, Kataoka Y,. Shimizu Y, Kambara T, Uemura Y, Yuasa D, Matsuo K, Hayakawa S,. Hiramatsu-Ito M, Murohara T, Ouchi N;. J Biol Chem. 2014;289:14132-14144.. [2]. 20969804. Spatio-temporal expression of a novel neuron-derived. neurotrophic factor (NDNF) in mouse brains during development.. Kuang XL, Zhao XM, Xu HF, Shi YY, Deng JB, Sun GT;. BMC Neurosci. 2010;11:137. (from Pfam)

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2024-08-14

The multifunctional fibrillar adhesin CshA, which mediates binding to both host molecules and other microorganisms, is an important determinant of colonization by Streptococcus gordonii, an oral commensal and opportunistic pathogen of animals and humans. CshA binds the high-molecular-weight glycoprotein fibronectin (Fn) via an N-terminal non-repetitive region, and this protein-protein interaction has been proposed to promote S. gordonii colonization at multiple sites within the host. This 259-kDa polypeptide is organized in the form of a leader peptide (residues 1-41), a non-repetitive region (residues 42-778), 17 repeat domains (R1-R17, each about 101-aa residues), and a C-terminal cell wall anchor. The non-repetitive Fn-binding region of CshA in turn is composed of three distinct domains, designated as non-repetitive domain 1 (NR1, CshA(42-222)), non-repetitive domain 2 (NR2, CshA(223-540)), and non-repetitive domain 3 (NR3, CshA(582-814)). The NR2 domain of CshA is shown to adopt a globular structure with a lectin-like fold and a ligand-binding site on its surface with structural homologues identified as those involved in binding carbohydrates or glycoproteins [1]. [1]. 27920201. The Streptococcus gordonii Adhesin CshA Protein Binds Host. Fibronectin via a Catch-Clamp Mechanism.. Back CR, Sztukowska MN, Till M, Lamont RJ, Jenkinson HF, Nobbs. AH, Race PR;. J Biol Chem. 2017;292:1538-1549. (from Pfam)

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2024-08-14

This is the second domain (C2) located in the C-terminal region found in antigen I/II type adhesin protein AspA from S. pyogenes. Together with C3, these two domains form an elongated structure, each domain adopts the DEv-IgG fold. Similar to the classical IgG folds, it is comprised of two major antiparallel beta-sheets, designated ABED and CFG. For the C2-domain, there are two additional strands on the CFG sheet. Furthermore, sheets ABED and CFG are interconnected by several cross-connecting loops and one alpha-helix (DH1). The side chains of D982 and N996 in the C2-domain are involved in hydrogen bonding with the side chains of R1264 and N1295 in the C3 domain. Main chain hydrogen bonding can also be observed between S992 in C2 and N1189/G1191 in C3, furthermore stabilizing the interaction between the domains. The C2 domain contains one bound metal ion, modeled as Ca2+, and both the C2- and C3-domains are stabilized by conserved isopeptide bonds, which connect the beta-sheets of the central DEv-IgG motifs [1].Other members of this family include Major cell-surface adhesin PAc from Streptococcus mutans and SspB from Streptococcus gordonii. [1]. 24918040. Structure of the C-terminal domain of AspA (antigen I/II-family). protein from Streptococcus pyogenes.. Hall M, Nylander S, Jenkinson HF, Persson K;. FEBS Open Bio. 2014;4:283-289. (from Pfam)

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2024-08-14

This domain is found in BspA protein present in Streptococcus agalactiae. BspA is an antigen I/II family polypeptide that confers adhesion linked to pathogenesis in group B Streptococcus. This domain is referred to as the variable domain (BspA-V). BspA-V is responsible for binding to scavenger receptor gp340. BspA-V adopts a fold that is distinct from those of other AgI/II family polypeptide variable domains [1]. [1]. 27311712. Structural and Functional Analysis of Cell Wall-anchored. Polypeptide Adhesin BspA in Streptococcus agalactiae.. Rego S, Heal TJ, Pidwill GR, Till M, Robson A, Lamont RJ,. Sessions RB, Jenkinson HF, Race PR, Nobbs AH;. J Biol Chem. 2016;291:15985-16000. (from Pfam)

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2024-08-14

IN certain plant and yeast proteins, the DnaJ-1 proteins have a three-domain structure. The x-domain lies between the N-terminal DnaJ and the C-terminal Z domains. The exact function is not known. [1]. 9679141. The cytosolic DnaJ-like protein djp1p is involved specifically. in peroxisomal protein import.. Hettema EH, Ruigrok CC, Koerkamp MG, van den Berg M, Tabak HF,. Distel B, Braakman I;. J Cell Biol. 1998;142:421-434. (from Pfam)

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2024-08-14

These proteins catalyse the reversible transfer of an amino group from the amino acid substrate to an acceptor alpha-keto acid. They require pyridoxal 5'-phosphate (PLP) as a cofactor to catalyse this reaction. Trans-amination reactions are of central importance in amino acid metabolism and in links to carbohydrate and fat metabolism. This class of amino-transferases acts as dimers in a head-to-tail configuration. It has been demonstrated that these proteins are aspartate amino-transferases from Bacteria (Jansen, R.S. et al. Nat Commun 11, 1960 (2020)) [1]. [1]. 27355211. Structural Insights into a Novel Class of Aspartate. Aminotransferase from Corynebacterium glutamicum.. Son HF, Kim KJ;. PLoS One. 2016;11:e0158402. (from Pfam)

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2024-08-14

This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 558 and 775 amino acids in length. There is a conserved TGG sequence motif. PNGase A is a protein which cleaves glycopeptides. [1]. 8940027. Haemonchus contortus glycoproteins contain N-linked. oligosaccharides with novel highly fucosylated core structures.. Haslam SM, Coles GC, Munn EA, Smith TS, Smith HF, Morris HR,. Dell A;. J Biol Chem. 1996;271:30561-30570. (from Pfam)

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2024-08-14

The UNC-45 or small muscle protein 1 of C.elegans is expressed in two forms from different genomic positions in mammals, as a general tissue protein UNC-45a and a specific form Unc-45b expressed only in striated and skeletal muscle. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) domains towards their N-terminal, a UCS domain at the C-terminal that contains a number of Arm repeats Pfam:PF00514 and this central region of approximately 400 residues. Both the general form and the muscle form of UNC-45 function in myotube formation through cell fusion. Myofibril formation requires both GC and SM UNC-45, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organised myofibrils [1]. The S. pombe Rng3p, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins [2]. Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90. The exact function of this central region is not known [3]. [1]. 12356907. Two mammalian UNC-45 isoforms are related to distinct. cytoskeletal and muscle-specific functions.. Price MG, Landsverk ML, Barral JM, Epstein HF;. J Cell Sci. 2002;115:4013-4023.. [2]. 18523008. Yeast UCS proteins promote actomyosin interactions and limit. myosin turnover in cells.. Lord M, Sladewski TE, Pollard TD;. Proc Natl Aca. TRUNCATED at 1650 bytes (from Pfam)

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2024-08-14

This domain is found towards the N-terminal of Neuron-derived neurotrophic factor (NDNF) which contains the first fibronectin type III domain and one of the predicted N-linked glycosylation sites [1,2]. NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularization. [1]. 20969804. Spatio-temporal expression of a novel neuron-derived. neurotrophic factor (NDNF) in mouse brains during development.. Kuang XL, Zhao XM, Xu HF, Shi YY, Deng JB, Sun GT;. BMC Neurosci. 2010;11:137.. [2]. 24706764. Neuron-derived neurotrophic factor functions as a novel. modulator that enhances endothelial cell function and. revascularization processes.. Ohashi K, Enomoto T, Joki Y, Shibata R, Ogura Y, Kataoka Y,. Shimizu Y, Kambara T, Uemura Y, Yuasa D, Matsuo K, Hayakawa S,. Hiramatsu-Ito M, Murohara T, Ouchi N;. J Biol Chem. 2014;289:14132-14144. (from Pfam)

Date:

2024-08-14

This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation [1]. [1]. 12832055. Homodimerization through coiled-coil regions enhances activity. of the myotonic dystrophy protein kinase.. Zhang R, Epstein HF;. FEBS Lett. 2003;546:281-287. (from Pfam)

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2024-08-14

The FrsA-like family includes FrsA, an esterase found to have the alpha/beta-hydrolase fold [1,2,3]. t also includes the hydrolytic polyketide shortening protein Ayg1 from fungi [4], 2,6-dihydropseudooxynicotine hydrolase from Paenarthrobacter nicotinovorans [5] and Fus2 from Gibberella species [6]. The enzyme 2,6-dihydroxy-pseudo-oxynicotine hydrolase is involved in the nicotine-degradation pathway of Arthrobacter nicotinovorans [5]. Fus2 is part of the gene cluster that mediates the biosynthesis of the mycotoxin fusarin C. Fus2 catalyses closure of the 2-pyrrolidone ring of the intermediate 20-hydroxy-prefusarin to form another intermediate, 20-hydroxy-fusarin, which is then oxidized by Fus8 [6]. [1]. 30951551. Purification and biochemical characterization of FrsA protein. from Vibrio vulnificus as an esterase.. Wang X, Li ZM, Li Q, Shi M, Bao L, Xu D, Li Z;. PLoS One. 2019;14:e0215084.. [2]. 23452154. Computational, structural, and kinetic evidence that Vibrio. vulnificus FrsA is not a cofactor-independent pyruvate. decarboxylase.. Kellett WF, Brunk E, Desai BJ, Fedorov AA, Almo SC, Gerlt JA,. Rothlisberger U, Richards NG;. Biochemistry. 2013;52:1842-1844.. [3]. 21623357. FrsA functions as a cofactor-independent decarboxylase to. control metabolic flux.. Lee KJ, Jeong CS, An YJ, Lee HJ, Park SJ, Seok YJ, Kim P, Lee. JH, Lee KH, Cha SS;. Nat Chem Biol. 2011;7:434-436.. [4]. 15310761. Hydrolytic polyketide shortening by ayg1p, a novel enzyme. involved in fungal melanin biosynthesis.. Fujii I, Yasuoka Y, Tsai HF, Chang YC, Kwon-Chung KJ, Ebizuka Y;. J Biol Chem. 2004;279:44613-44620.. [5]. 17275835. Structure and action of. TRUNCATED at 1650 bytes (from Pfam)

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2024-08-14

This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with Pfam:PF00664. Mutations in this domain in Swiss:P28288 are believed responsible for Zellweger Syndrome-2 [1]; mutations in Swiss:P33897 are responsible for recessive X-linked adrenoleukodystrophy [2]. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids [3]. [1]. 1301993. Mutations in the 70K peroxisomal membrane protein gene in. Zellweger syndrome.. Gartner J, Moser H, Valle D;. Nat Genet 1992;1:16-23.. [2]. 8441467. Putative X-linked adrenoleukodystrophy gene shares unexpected. homology with ABC transporters.. Mosser J, Douar AM, Sarde CO, Kioschis P, Feil R, Moser H,. Poustka AM, Mandel JL, Aubourg P;. Nature 1993;361:726-730.. [3]. 8670886. The ABC transporter proteins Pat1 and Pat2 are required for. import of long-chain fatty acids into peroxisomes of. Saccharomyces cerevisiae.. Hettema EH, van Roermund CW, Distel B, van den Berg M, Vilela C,. Rodrigues-Pousada C, Wanders RJ, Tabak HF;. EMBO J 1996;15:3813-3822. (from Pfam)

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2024-08-14

Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. Homologues to this peptidase domain, which corresponds to Merops family M56, are also found in a number of other bacterial genome sequences. [1]. 11245199. Microbiology. Signaling antibiotic resistance in staphylococci.. Archer GL, Bosilevac JM;. Science 2001;291:1915-1916.. [2]. 11239156. A proteolytic transmembrane signaling pathway and resistance to. beta-lactams in staphylococci.. Zhang HZ, Hackbarth CJ, Chansky KM, Chambers HF;. Science 2001;291:1962-1965.. [3]. 9164468. Mechanisms of methicillin resistance in staphylococci.. Brakstad OG, Maeland JA;. APMIS 1997;105:264-276.. [4]. 23733187. A novel family of soluble minimal scaffolds provides structural. insight into the catalytic domains of integral membrane. metallopeptidases.. Lopez-Pelegrin M, Cerda-Costa N, Martinez-Jimenez F,. Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA,. Lopez-Otin C, Arolas JL, Gomis-Ruth FX;. J Biol Chem. 2013;288:21279-21294. (from Pfam)

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2024-08-14

This domain is found in peptide chain release factors. [1]. 19064930. Crystal structure of a translation termination complex formed. with release factor RF2.. Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu. J, Trakhanov S, Scott WG, Noller HF;. Proc Natl Acad Sci U S A. 2008;105:19684-19689. (from Pfam)

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2024-08-14

Thymidylate synthase complementing protein (Thy1) complements the thymidine growth requirement of the organisms in which it is found, but shows no homology to thymidylate synthase. The bacterial members of this family at least are flavin-dependent thymidylate synthases [2,3,4]. [1]. 9665876. Complete genome sequence of Treponema pallidum, the syphilis. spirochete [see comments]. Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson. R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E,. Hardham JM, McLeod MP, Salzberg S, Peterson J, Khalak H,. Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L,. Artiach P,. Science 1998;281:375-388.. [2]. 12029065. An alternative flavin-dependent mechanism for thymidylate. synthesis.. Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl. U;. Science. 2002;297:105-107.. [3]. 15046578. Two distinct pathways for thymidylate (dTMP) synthesis in. (hyper)thermophilic Bacteria and Archaea.. Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U,. Myllykallio H;. Biochem Soc Trans. 2004;32:231-235.. [4]. 17890305. Flavin-dependent thymidylate synthase ThyX activity:. implications for the folate cycle in bacteria.. Leduc D, Escartin F, Nijhout HF, Reed MC, Liebl U, Skouloubris. S, Myllykallio H;. J Bacteriol. 2007;189:8537-8545. (from Pfam)

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2024-08-14

This is the N-terminal domain found in hepatic lectins, also known as Asialoglycoprotein receptors (ASGRs). ASGRs function as scavengers to mediate the endocytosis of plasma glycoproteins with terminal galactose and N-acetylgalactosamine units [1,2,3]. ASGR is composed of a major (ASGR1) and a minor (ASGR2) subunits, both of which are type II, single-pass transmembrane proteins [1,2]. ASGR is highly expressed in liver but has been also identified in human peripheral blood monocytes, representing a mobile pool of the receptor reaching distant sites from the liver to play a scavenger function where there is an infection or a damaged tissue [2]. This domain includes the short, single transmembrane domain and the stalk region which mediates the oligomerisation between subunits. [1]. 1785139. Recognition of complex oligosaccharides by the multi-subunit. asialoglycoprotein receptor.. Lodish HF;. Trends Biochem Sci 1991;16:374-377.. [2]. 22919488. ASGR1 and ASGR2, the Genes that Encode the Asialoglycoprotein. Receptor (Ashwell Receptor), Are Expressed in Peripheral Blood. Monocytes and Show Interindividual Differences in Transcript. Profile.. Harris RL, van den Berg CW, Bowen DJ;. Mol Biol Int. 2012;2012:283974.. [3]. 29069408. Asialoglycoprotein receptor 1 mediates productive uptake of. N-acetylgalactosamine-conjugated and unconjugated. phosphorothioate antisense oligonucleotides into liver. hepatocytes.. Tanowitz M, Hettrick L, Revenko A, Kinberger GA, Prakash TP,. Seth PP;. Nucleic Acids Res. 2017;45:12388-12400. (from Pfam)

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2024-08-14

Bacterial ribosomal protein S20 interacts with 16S rRNA [1]. [1]. 3373529. Interaction of proteins S16, S17 and S20 with 16 S ribosomal. RNA.. Stern S, Changchien LM, Craven GR, Noller HF;. J Mol Biol 1988;200:291-299. (from Pfam)

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2024-08-14

This is a family of proteins that are flavin-dependent thymidylate synthases. [1]. 12029065. An alternative flavin-dependent mechanism for thymidylate. synthesis.. Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl. U;. Science. 2002;297:105-107.. [2]. 15046578. Two distinct pathways for thymidylate (dTMP) synthesis in. (hyper)thermophilic Bacteria and Archaea.. Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U,. Myllykallio H;. Biochem Soc Trans. 2004;32:231-235.. [3]. 17890305. Flavin-dependent thymidylate synthase ThyX activity:. implications for the folate cycle in bacteria.. Leduc D, Escartin F, Nijhout HF, Reed MC, Liebl U, Skouloubris. S, Myllykallio H;. J Bacteriol. 2007;189:8537-8545. (from Pfam)

Date:

2024-08-14