Protein Family Models

glycoside hydrolase family 28 protein such as polygalacturonase that catalyzes the random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans, and exo-poly-alpha-D-galacturonosidase which catalyzes the hydrolysis of pectic acid from the non-reducing end, releasing digalacturonate

Date:

2024-02-09

glycoside hydrolase family 28 protein such as polygalacturonase that catalyzes the random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans, and exo-poly-alpha-D-galacturonosidase which catalyzes the hydrolysis of pectic acid from the non-reducing end, releasing digalacturonate

Date:

2024-02-09

bifunctional glycosyltransferase family 2 protein/CDP-glycerol:glycerophosphate glycerophosphotransferase is a glycosyltransferase (GT) containing both family A (GTA) and family B (GTB) folds, and may be involved in the poly(glycerol phosphate) teichoic acid biosynthesis pathway, which is part of cell wall biogenesis

Date:

2024-02-09

This is a cysteine rich domain which contains four zinc-binding regions (binding five zinc ions). Family members include human CHFR which interacts with Poly(ADP-ribose) (PAR) through a 20-amino acid PAR binding zinc finger region (PBZ) found at the C-terminal end of this cysteine-rich domain (i.e. the 4th region towards the C-terminal). CHFR lacking PBZ does not co-localize with nuclear PAR foci in interphase cells and cannot rescue antephase checkpoint function despite retaining autoubiquitination activity. Hence it has been suggested that the CHFR-PAR interaction is an important part of the antephase checkpoint and could form part of the checkpoint sensor for cellular stress and microtubule poisons or be required for proper localization of CHFR. The PBZ region of CHFR contains two adenine binding sites [1]. [1]. 20880844. Structural basis of poly(ADP-ribose) recognition by the. multizinc binding domain of checkpoint with forkhead-associated. and RING Domains (CHFR).. Oberoi J, Richards MW, Crumpler S, Brown N, Blagg J, Bayliss R;. J Biol Chem. 2010;285:39348-39358. (from Pfam)

Date:

2024-08-14

This is a GW domain found in the C-terminal of InlB proteins which belong to the extended family of internalin proteins found in Listeria [1]. These 80 residue GW domains are unique to InlB among the internalins but are present in other proteins of Gram-positive bacteria [2]. GW domains (named after a GlyTryp dipeptide) are structurally and evolutionary related to SH3 domains [1]. Despite of this, GW domains are unlikely to act as functional mimics of SH3 domains since their potential proline-binding sites are blocked or destroyed [2]. They are highly basic and interact with poly-anions. The GW domains are responsible for the non-covalent attachment to the bacterial cell surface through binding to lipoteichoic acid. The GW domains alone do not stimulate uptake, but they synergize with the Met-binding internalin domain [1]. [1]. 21242015. Structural insights into Met receptor activation.. Niemann HH;. Eur J Cell Biol. 2011;90:972-981.. [2]. 12411480. GW domains of the Listeria monocytogenes invasion protein InlB. are SH3-like and mediate binding to host ligands.. Marino M, Banerjee M, Jonquieres R, Cossart P, Ghosh P;. EMBO J. 2002;21:5623-5634. (from Pfam)

Date:

2024-08-14

The residues upstream of this domain are the probable palmitoylation sites, particularly two cysteines. The domain has a putative PEST site at the very start that seems to be responsible for poly-ubiquitination [1]. PEST domains are polypeptide sequences enriched in proline (P), glutamic acid (E), serine (S) and threonine (T) that target proteins for rapid destruction. The whole domain, in conjunction with a C-terminal domain of the longer protein, is necessary for dimerisation of the whole protein [2]. [1]. 8755249. PEST sequences and regulation by proteolysis.. Rechsteiner M, Rogers SW;. Trends Biochem Sci. 1996;21:267-271.. [2]. 18215622. Molecular dissociation of the role of PSD-95 in regulating. synaptic strength and LTD.. Xu W, Schluter OM, Steiner P, Czervionke BL, Sabatini B, Malenka. RC;. Neuron. 2008;57:248-262. (from Pfam)

Date:

2024-08-14

This family of proteins play a role in capsule biosynthesis. They are essential for gamma-polyglutamic acid (PGA) production [1]. [1]. 11751809. Characterization of the Bacillus subtilis ywsC gene, involved in. gamma-polyglutamic acid production.. Urushibata Y, Tokuyama S, Tahara Y;. J Bacteriol. 2002;184:337-343. (from Pfam)

Date:

2024-08-14

The Tbk1/Ikki binding domain (TBD) is a 40 amino acid domain able to bind kinases, has been found to be essential for poly(I:C)-induced IRF activation [1]. The domain is found in SINTBAD, TANK and NAP1 protein. This domain is predicted to form an a-helix with residues essential for kinase binding clustering on one side [1]. [1]. 17568778. SINTBAD, a novel component of innate antiviral immunity, shares. a TBK1-binding domain with NAP1 and TANK.. Ryzhakov G, Randow F;. EMBO J. 2007;26:3180-3190. (from Pfam)

Date:

2024-08-14

This family consists of bacterial cutinases (EC:3.1.1.74), which catalyse the hydrolysis of cutin, a polyester that forms the structure of plant cuticle [1,2]. These enzymes also show esterase activity towards p-nitrophenol-linked aliphatic esters [3,4]. Cutinase est2 can also depolymerize the synthetic polyesters poly(epsilon-caprolactone) (PCL), poly(butylene succinate-co-adipate) (PBSA), poly(butylene succinate) (PBS), and poly(lactic acid) (PLA) [5,6,7]. Members of this family are able to degrade the plastic poly(ethylene terephthalate) (PET). [1]. 24728714. Structural and functional studies on a thermostable polyethylene. terephthalate degrading hydrolase from Thermobifida fusca.. Roth C, Wei R, Oeser T, Then J, Follner C, Zimmermann W, Strater. N;. Appl Microbiol Biotechnol. 2014;98:7815-7823.. [2]. 28671263. Small cause, large effect: Structural characterization of. cutinases from Thermobifida cellulosilytica.. Ribitsch D, Hromic A, Zitzenbacher S, Zartl B, Gamerith C,. Pellis A, Jungbauer A, Lyskowski A, Steinkellner G, Gruber K,. Tscheliessnig R, Herrero Acero E, Guebitz GM;. Biotechnol Bioeng. 2017;114:2481-2488.. [3]. 25910960. Comparison of genetic structures and biochemical properties of. tandem cutinase-type polyesterases from Thermobifida alba. AHK119.. Thumarat U, Kawabata T, Nakajima M, Nakajima H, Sugiyama A,. Yazaki K, Tada T, Waku T, Tanaka N, Kawai F;. J Biosci Bioeng. 2015;120:491-497.. [4]. 33387709. Decolorization of molasses alcohol wastewater by thermophilic. hydrolase with practical application value.. Zhang Z, Wang W, Li D, Xiao J, Wu L, Geng X, Wu G, Zeng Z, Hu J;. Bioresour Technol. 2021;323:1. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This is the catalytic domain found in the endoplasmic reticulum (ER) -bound oxygenases mpaB' (MPAB2) and mpaB (MPAB) from Penicillium roqueforti and Penicillium brevicompactum and in the rubber oxygenase (Lcp) from Streptomyces sp., which contains highly conserved arginine and histidine residues. Structural analysis from Lcp revealed that Arg164, Thr168 and His198 are crucial active site residues [1]. The mpaB and mpaB' are part of the gene cluster that mediates the biosynthesis of mycophenolic acid (MPA) [2]. Lcp (Latex clearing proteins) is a rubber oxygenase that catalyses the extracellular cleavage of poly (cis-1,4-isoprene) [1,3]. This domain is also present in uncharacterised proteins from Mycobacterium sp. and hypothetical proteins, mainly from bacteria and fungi. [1]. 28733658. Structural and Functional Analysis of Latex Clearing Protein. (Lcp) Provides Insight into the Enzymatic Cleavage of Rubber.. Ilcu L, Rother W, Birke J, Brausemann A, Einsle O, Jendrossek D;. Sci Rep. 2017;7:6179.. [2]. 31209052. Compartmentalized biosynthesis of mycophenolic acid.. Zhang W, Du L, Qu Z, Zhang X, Li F, Li Z, Qi F, Wang X, Jiang Y,. Men P, Sun J, Cao S, Geng C, Qi F, Wan X, Liu C, Li S;. Proc Natl Acad Sci U S A. 2019;116:13305-13310.. [3]. 25819959. Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30 Is a. b-Type Cytochrome and Differs from Rubber Oxygenase A (RoxA) in. Its Biophysical Properties.. Birke J, Rother W, Jendrossek D;. Appl Environ Microbiol. 2015;81:3793-3799. (from Pfam)

Date:

2024-08-14

This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. (from Pfam)

Date:

2024-08-14

This family represents the N-terminal region of the bacterial poly-beta-hydroxybutyrate polymerase (PhaC). Polyhydroxyalkanoic acids (PHAs) are carbon and energy reserve polymers produced in some bacteria when carbon sources are plentiful and another nutrient, such as nitrogen, phosphate, oxygen, or sulfur, becomes limiting. PHAs composed of monomeric units ranging from 3 to 14 carbons exist in nature. When the carbon source is exhausted, PHA is utilised by the bacterium. PhaC links D-(-)-3-hydroxybutyrl-CoA to an existing PHA molecule by the formation of an ester bond [1]. This family appears to be a partial segment of an alpha/beta hydrolase domain. [1]. 10427049. Cloning, molecular analysis, and expression of the. polyhydroxyalkanoic acid synthase (phaC) gene from. Chromobacterium violaceum.. Kolibachuk D, Miller A, Dennis D;. Appl Environ Microbiol 1999;65:3561-3565. (from Pfam)

Date:

2024-08-14

This family represents the C-terminus of bacterial poly(3-hydroxybutyrate) (PHB) de-polymerase. This degrades PHB granules to oligomers and monomers of 3-hydroxy-butyric acid. [1]. 12813072. Ralstonia eutropha H16 encodes two and possibly three. intracellular Poly[D-(-)-3-hydroxybutyrate] depolymerase genes.. York GM, Lupberger J, Tian J, Lawrence AG, Stubbe J, Sinskey AJ;. J Bacteriol 2003;185:3788-3794. (from Pfam)

Date:

2024-08-14

E. coli YceI is a base-induced periplasmic protein [1]. The recent structure of a member of this family shows that it binds to poly-isoprenoid [2]. The structure consists of an extended, eight-stranded, antiparallel beta-barrel that resembles the lipocalin fold. [1]. 12107143. pH-Dependent Expression of Periplasmic Proteins and Amino Acid. Catabolism in Escherichia coli.. Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN,. Slonczewski JL;. J Bacteriol 2002;184:4246-4258.. [2]. 15741337. Crystal structure of a novel polyisoprenoid-binding protein from. Thermus thermophilus HB8.. Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY,. Kuramitsu S, Shirouzu M, Yokoyama S;. Protein Sci. 2005;14:1004-1010. (from Pfam)

Date:

2024-08-14

The WecG member of this family, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan [1, 2, 3, 4, 5, 6, 7]. [1]. 8830246. Characterization of cpsF and its product CMP-N-acetylneuraminic. acid synthetase, a group B streptococcal enzyme that can. function in K1 capsular polysaccharide biosynthesis in. Escherichia coli.. Haft RF, Wessels MR, Mebane MF, Conaty N, Rubens CE;. Mol Microbiol. 1996;19:555-563.. [2]. 11673418. Identification of the structural gene for the TDP-Fuc4NAc:lipid. II Fuc4NAc transferase involved in synthesis of enterobacterial. common antigen in Escherichia coli K-12.. Rahman A, Barr K, Rick PD;. J Bacteriol 2001;183:6509-6516.. [3]. 12618464. Identification and biosynthesis of cyclic enterobacterial common. antigen in Escherichia coli.. Erbel PJ, Barr K, Gao N, Gerwig GJ, Rick PD, Gardner KH;. J Bacteriol. 2003;185:1995-2004.. [4]. 18156271. Localization and interactions of teichoic acid synthetic enzymes. in Bacillus subtilis.. Formstone A, Carballido-Lopez R, Noirot P, Errington J,. Scheffers DJ;. J Bacteriol. 2008;190:1812-1821.. [5]. 16953575. Acceptor substrate selectivity. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

Wall-associated teichoic acids are a heterogeneous class of phosphate-rich polymers that are covalently linked to the cell wall peptidoglycan of gram-positive bacteria. They consist of a main chain of phosphodiester-linked polyols and/or sugar moieties attached to peptidoglycan via a linkage unit. CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase is responsible for the polymerisation of the main chain of the teichoic acid by sequential transfer of glycerol-phosphate units from CDP-glycerol to the linkage unit lipid [1]. [1]. 10648531. Molecular analysis of the tagF gene, encoding. CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase of. Staphylococcus epidermidis ATCC 14990.. Fitzgerald SN, Foster TJ;. J Bacteriol 2000;182:1046-1052. (from Pfam)

Date:

2024-08-14

This family consist of rotaviral non-structural RNA binding protein 34 (NS34 or NSP3). The NSP3 protein has been shown to bind viral RNA. The NSP3 protein consists of 3 conserved functional domains; a basic region which binds ssRNA, a region containing heptapeptide repeats mediating oligomerisation and a leucine zipper motif [2]. NSP3 may play a central role in replication and assembly of genomic RNA structures [2]. Rotaviruses have a dsRNA genome and are a major cause cause of acute gastroenteritis in the young of many species [1]. The rotavirus non-structural protein NSP3 is a sequence-specific RNA binding protein that binds the nonpolyadenylated 3' end of the rotavirus mRNAs. NSP3 also interacts with the translation initiation factor eIF4GI and competes with the poly(A) binding protein [3]. [1]. 7871749. Comparative nucleotide and amino acid sequence analysis of the. sequence- specific RNA-binding rotavirus nonstructural protein. NSP3.. Rao CD, Das M, Ilango P, Lalwani R, Rao BS, Gowda K;. Virology 1995;207:327-333.. [2]. 1326821. Characterization of an oligomerization domain and RNA-binding. properties on rotavirus nonstructural protein NS34.. Mattion NM, Cohen J, Aponte C, Estes MK;. Virology 1992;190:68-83.. [3]. 9755181. Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and. evicts the poly(A) binding protein from eIF4F.. Piron M, Vende P, Cohen J, Poncet D;. EMBO J 1998;17:5811-5821. (from Pfam)

Date:

2024-08-14

This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily. [1]. 1438224. Identification of the gene for an Escherichia coli poly(A). polymerase.. Cao GJ, Sarkar N;. Proc Natl Acad Sci U S A 1992;89:10380-10384. (from Pfam)

Date:

2024-08-14

Gene:

phaB

Date:

2023-08-31

class I poly(R)-hydroxyalkanoic acid synthase similar to poly(3-hydroxyalkanoate) polymerase subunit PhaC, which polymerizes D(-)-3-hydroxybutyryl-CoA to produce polyhydroxybutyrate (PHB)

Date:

2023-06-04