Protein Family Models

1,4-alpha-glucan-branching protein transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain

Date:

2024-02-09

hydroxyisourate hydrolase catalyzes the hydrolysis of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) in the second step of a three-step ureide pathway

Date:

2024-02-09

This is the dimerization domain (DD) found in Yos9 proteins in yeast. Structural analysis revealed that this domain contributes to self association of Yos9. The overall fold of the domain can be classified as an alpha-beta-roll architecture, comprising two alpha-helices and seven beta-strands [1]. [1]. 22262864. Structural and biochemical basis of Yos9 protein dimerization. and possible contribution to self-association of. 3-hydroxy-3-methylglutaryl-coenzyme A reductase degradation. ubiquitin-ligase complex.. Hanna J, Schutz A, Zimmermann F, Behlke J, Sommer T, Heinemann. U;. J Biol Chem. 2012;287:8633-8640. (from Pfam)

Date:

2024-08-14

TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by Pfam:PF00205. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria [1]. [1]. 18983854. Specificity and reactivity in menaquinone biosynthesis: the. structure of Escherichia coli MenD. (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxyla. te synthase).. Dawson A, Fyfe PK, Hunter WN;. J Mol Biol. 2008;384:1353-1368. (from Pfam)

Date:

2024-08-14

This model describes the N-terminal domain of a group of mostly uncharacterised proteins, including 5-methylcytosine-specific restriction enzyme B (also known as MrcB) from E. coli. MrcB recognises N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue [1]. The N-terminal domain of MrcB has been shown to be a DNA-binding domain, and the crystal structure has been solved [2]. [1]. 7781618. McrB: a prokaryotic protein specifically recognizing DNA. containing modified cytosine residues.. Kruger T, Wild C, Noyer-Weidner M;. EMBO J. 1995;14:2661-2669.. [2]. 22570415. The recognition domain of the methyl-specific endonuclease McrBC. flips out 5-methylcytosine.. Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V;. Nucleic Acids Res. 2012;40:7552-7562. (from Pfam)

Date:

2024-08-14

This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group [1]. [1]. 23790488. Structural and stereochemical analysis of a modular polyketide. synthase ketoreductase domain required for the generation of a. cis-alkene.. Bonnett SA, Whicher JR, Papireddy K, Florova G, Smith JL,. Reynolds KA;. Chem Biol. 2013;20:772-783. (from Pfam)

Date:

2024-08-14

The proteins in this family are OHCU decarboxylase - enzymes of the purine catabolism that catalyse the conversion of OHCU into S(+)-allantoin [1]. This is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase (Pfam:PF01014) and step two is catalysed by HIUases (Pfam:PF00576). [1]. 16462750. Completing the uric acid degradation pathway through. phylogenetic comparison of whole genomes.. Ramazzina I, Folli C, Secchi A, Berni R, Percudani R;. Nat Chem Biol. 2006;2:144-148. (from Pfam)

Date:

2024-08-14

This family consists of several bacterial tRNA-(MS(2)IO(6)A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species [1-2]. [1]. 8253666. Isolation of the gene (miaE) encoding the hydroxylase involved. in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of. Salmonella typhimurium and characterization of mutants.. Persson BC, Bjork GR;. J Bacteriol 1993;175:7776-7785.. [2]. 17679698. tRNA-modifying MiaE protein from Salmonella typhimurium is a. nonheme diiron monooxygenase.. Mathevon C, Pierrel F, Oddou JL, Garcia-Serres R, Blondin G,. Latour JM, Menage S, Gambarelli S, Fontecave M, Atta M;. Proc Natl Acad Sci U S A. 2007;104:13295-13300. (from Pfam)

Gene:

miaE

Date:

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)

Date:

2024-08-14

Budding yeast Mpo1 is a dioxygenase that catalyzes the alpha-oxidation of a 2-hydroxy fatty acid in an Fe2+-dependent manner [1]. This entry also includes Mpo1 homologues from bacteria, fungi and plants. Their function is not clear. [1]. 30530523. Yeast Mpo1 Is a Novel Dioxygenase That Catalyzes the. alpha-Oxidation of a 2-Hydroxy Fatty Acid in an Fe(2+)-Dependent. Manner.. Seki N, Mori K, Kitamura T, Miyamoto M, Kihara A;. Mol Cell Biol. 2019; [Epub ahead of print] (from Pfam)

Date:

2024-08-14

In the unicellular biflagellated alga, Chlamydomonas reinhardtii, gametolysin, a zinc-containing metallo-protease, is responsible for the degradation of the cell wall. Homologues of gametolysin have also been reported in the simple multicellular organism, Volvox. [1]. 12073093. Genealogical relationships among laboratory strains of. Chlamydomonas reinhardtii as inferred from matrix. metalloprotease genes.. Kubo T, Abe J, Saito T, Matsuda Y;. Curr Genet 2002;41:115-122.. [2]. 11680823. Two tandemly-located matrix metalloprotease genes with different. expression patterns in the chlamydomonas sexual cell cycle.. Kubo T, Saito T, Fukuzawa H, Matsuda Y;. Curr Genet 2001;40:136-143.. [3]. 12034745. An extracellular matrix-localized metalloproteinase with an. exceptional QEXXH metal binding site prefers copper for. catalytic activity.. Heitzer M, Hallmann A;. J Biol Chem 2002;277:28280-28286.. [4]. 11489172. Transcriptional activation by the sexual pheromone and wounding:. a new gene family from Volvox encoding modular proteins with. (hydroxy)proline-rich and metalloproteinase homology domains.. Hallmann A, Amon P, Godl K, Heitzer M, Sumper M;. Plant J 2001;26:583-593. (from Pfam)

Date:

2024-08-14

The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation utilising ATP. Likewise hydroxyurea is inactivated by phosphorylation of the hydroxy group in the hydroxylamine moiety [1,2,3]. [1]. 3029728. Nucleotide sequence of the streptomycinphosphotransferase and. amidinotransferase genes from Streptomyces griseus.. Tohyama H, Okami Y, Umezawa H;. Nucleic Acids Res 1987;15:1819-1833.. [2]. 9211644. Bacterial resistance to aminoglycoside antibiotics.. Davies J, Wright GD;. Trends Microbiol 1997;5:234-240.. [3]. 1316866. A gene (hur) from Streptomyces aureofaciens, conferring. resistance to hydroxyurea, is related to genes encoding. streptomycin phosphotransferase.. Kormanec J, Farkasovsky M, Potuckova L, Godar S;. Gene 1992;114:133-137. (from Pfam)

Date:

2024-08-14

Aconitase X (AcnX) is a subfamily of Acn superfamily. It is encoded in the genomes of many archaea, proteobacteria and fungi. Among archaea, the pattern of aconitase X occurrence complements that of aconitase A such that together the two enzymes account for aconitase activity in all archaea [1]. This protein catalyzes the dehydration of cis-3-hydroxy-L-proline to delta1-pyrroline-2-carboxylate [2]. [1]. 14568143. Filling a gap in the central metabolism of archaea: prediction. of a novel aconitase by comparative-genomic analysis.. Makarova KS, Koonin EV;. FEMS Microbiol Lett. 2003;227:17-23.. [2]. 27929065. Functional characterization of aconitase X as a. cis-3-hydroxy-L-proline dehydratase.. Watanabe S, Tajima K, Fujii S, Fukumori F, Hara R, Fukuda R,. Miyazaki M, Kino K, Watanabe Y;. Sci Rep. 2016;6:38720. (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

The MCRA (myosin-cross-reactive antigen) family of proteins were thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis[1]. More recent work shows that these proteins act as hydratase enzymes that convert linoleic acid and oleic acid to their respective 10-hydroxy derivatives. It has been suggested that MCRA proteins catalyse the first step in conjugated linoleic acid production [2]. Proteins in this family act in an FAD dependent manner [3]. The structure of a fatty acid double-bond hydratase from Lactobacillus acidophilus has been recently solved showing four structural domains. [1]. 8188369. Cloning and sequence analysis of a gene encoding a 67-kilodalton. myosin-cross-reactive antigen of Streptococcus pyogenes reveals. its similarity with class II major histocompatibility antigens.. Kil KS, Cunningham MW, Barnett LA;. Infect Immun 1994;62:2440-2449.. [2]. 22955678. Myosin-cross-reactive antigens from four different lactic acid. bacteria are fatty acid hydratases.. Yang B, Chen H, Song Y, Chen YQ, Zhang H, Chen W;. Biotechnol Lett. 2013;35:75-81.. [3]. 21329502. Myosin-cross-reactive antigen (MCRA) protein from. Bifidobacterium breve is a FAD-dependent fatty acid hydratase. which has a function in stress protection.. Rosberg-Cody E, Liavonchanka A, Gobel C, Ross RP, O'Sullivan O,. Fitzgerald GF, Feussner I, Stanton C;. BMC Biochem. 2011;12:9.. [4]. 20145247. Myosin cross-reactive antigen of Streptococcus pyogenes M49. encodes a fatty acid double bond hydratase that plays a role in. oleic acid detoxification and b. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain. [1]. 8873595. Interaction of pyridine nucleotide substrates with Escherichia. coli dihydrodipicolinate reductase: thermodynamic and structural. analysis of binary complexes.. Reddy SG, Scapin G, Blanchard JS;. Biochemistry 1996;35:13294-13302.. [2]. 9398235. Three-dimensional structure of Escherichia coli. dihydrodipicolinate reductase in complex with NADH and the. inhibitor 2,6-pyridinedicarboxylate.. Scapin G, Reddy SG, Zheng R, Blanchard JS;. Biochemistry 1997;36:15081-15088.. [3]. 7893645. Three-dimensional structure of Escherichia coli. dihydrodipicolinate reductase.. Scapin G, Blanchard JS, Sacchettini JC;. Biochemistry 1995;34:3502-3512. (from Pfam)

Date:

2024-08-14

Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037). [1]. 2207102. Cloning, sequence determination, and expression of the genes. encoding the subunits of the nickel-containing. 8-hydroxy-5-deazaflavin reducing hydrogenase from. Methanobacterium thermoautotrophicum delta H.. Alex LA, Reeve JN, Orme-Johnson WH, Walsh CT;. Biochemistry 1990;29:7237-7244.. [2]. 10751389. The F420H2 dehydrogenase from Methanosarcina mazei is a. Redox-driven proton pump closely related to NADH dehydrogenases.. Baumer S, Ide T, Jacobi C, Johann A, Gottschalk G, Deppenmeier. U;. J Biol Chem 2000;275:17968-17973.. [3]. 3531194. Cloning, expression, and nucleotide sequence of the formate. dehydrogenase genes from Methanobacterium formicicum.. Shuber AP, Orr EC, Recny MA, Schendel PF, May HD, Schauer NL,. Ferry JG;. J Biol Chem 1986;261:12942-12947. (from Pfam)

Date:

2024-08-14

Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the N termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037). [1]. 2207102. Cloning, sequence determination, and expression of the genes. encoding the subunits of the nickel-containing. 8-hydroxy-5-deazaflavin reducing hydrogenase from. Methanobacterium thermoautotrophicum delta H.. Alex LA, Reeve JN, Orme-Johnson WH, Walsh CT;. Biochemistry 1990;29:7237-7244.. [2]. 10751389. The F420H2 dehydrogenase from Methanosarcina mazei is a. Redox-driven proton pump closely related to NADH dehydrogenases.. Baumer S, Ide T, Jacobi C, Johann A, Gottschalk G, Deppenmeier. U;. J Biol Chem 2000;275:17968-17973.. [3]. 3531194. Cloning, expression, and nucleotide sequence of the formate. dehydrogenase genes from Methanobacterium formicicum.. Shuber AP, Orr EC, Recny MA, Schendel PF, May HD, Schauer NL,. Ferry JG;. J Biol Chem 1986;261:12942-12947. (from Pfam)

Date:

2024-08-14

In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesised by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway [2]. [1]. 1521767. Sequence and characterization of the gcpE gene of Escherichia. coli.. Baker J, Franklin DB, Parker J;. FEMS Microbiol Lett 1992;73:175-180.. [2]. 11274098. GcpE is involved in the 2-C-methyl-D-erythritol 4-phosphate. pathway of isoprenoid biosynthesis in Escherichia coli.. Altincicek B, Kollas AK, Sanderbrand S, Wiesner J, Hintz M, Beck. E, Jomaa H;. J Bacteriol 2001;183:2411-2416. (from Pfam)

Date:

2024-08-14

This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site [3]. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB. [1]. 11276424. The DNA-repair protein AlkB, EGL-9, and leprecan define new. families of 2-oxoglutarate- and iron-dependent dioxygenases.. Aravind L, Koonin EV;. Genome Biol 2001;2:RESEARCH0007.. [2]. 9211872. Cloning of the human prolyl 4-hydroxylase alpha subunit isoform. alpha(II) and characterization of the type II enzyme tetramer.. The alpha(I) and alpha(II) subunits do not form a mixed. alpha(I)alpha(II)beta2 tetramer.. Annunen P, Helaakoski T, Myllyharju J, Veijola J, Pihlajaniemi. T, Kivirikko KI;. J Biol Chem 1997;272:17342-17348.. [3]. 7753822. Cloning, baculovirus expression, and characterization of a. second mouse prolyl 4-hydroxylase alpha-subunit isoform:. formation of an alpha 2 beta 2 tetramer with the protein. disulfide-isomerase/beta subunit.. Helaakoski T, Annunen P, Vuori K, MacNeil IA, Pihlajaniemi T,. Kivirikko KI;. Proc Natl Acad Sci U S A 1995;92:4427-4431.. [4]. 7791906. Crystal structure of isopenicillin N synthase is the first from. a new structural family of enzymes.. Roach PL, Clifton IJ, Fulop V, Harlos K, Barton GJ, Hajdu J,. Andersson I,. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14