Protein Family Models

Gene:

sauS

Date:

2024-10-02

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

8-oxo-dGTP diphosphatase is a Nudix family hydrolase that catalyzes the hydrolysis of nucleoside triphosphates such as 8-oxo-dGTP, preventing A:T to C:G and G:C to T:A transversions

Date:

2024-02-09

This is the C-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain [1]. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity [2]. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK) [1]. [1]. 27402745. Assignment of function to a domain of unknown function: DUF1537. is a new kinase family in catabolic pathways for acid sugars.. Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S,. Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crecy-Lagard V,. Jacobson MP, Almo SC, Gerlt JA;. Proc Natl Acad Sci U S A. 2016;113:E4161-E4169.. [2]. 27294475. Members of a Novel Kinase Family (DUF1537) Can Recycle . TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This entry represents the C-terminal domain of mitochondrial D-glutamate cyclase, which converts D-glutamate to 5-oxo-D-proline [1]. This is a conserved domain also found in uncharacterised proteins from bacteria and archaea. Structural studies of the hypothetical protein TON_0340 from Thermococcus onnurineus revealed an active-site cavity harbouring a metal-binding site containing six invariant aspartate and glutamate residues that adopts an alpha/beta-structure [2]. Biochemical and mutational analysis show that TON_0340 is a Mn+2-dependent phosphatase [2]. [1]. 28266638. D-Glutamate is metabolized in the heart mitochondria.. Ariyoshi M, Katane M, Hamase K, Miyoshi Y, Nakane M, Hoshino A,. Okawa Y, Mita Y, Kaimoto S, Uchihashi M, Fukai K, Ono K,. Tateishi S, Hato D, Yamanaka R, Honda S, Fushimura Y, Iwai-Kanai. E, Ishihara N, Mita M, Homma H, Matoba S;. Sci Rep. 2017;7:43911.. [2]. 27907125. Identification of a Highly Conserved Hypothetical Protein. TON_0340 as a Probable Manganese-Dependent Phosphatase.. Sohn YS, Lee SG, Lee KH, Ku B, Shin HC, Cha SS, Kim YG, Lee HS,. Kang SG, Oh BH;. PLoS One. 2016;11:e0167549. (from Pfam)

Date:

2024-08-14

This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00676. There are two conserved sequence motifs: VPEP and RPG. This family is the alpha subunit of the E1 component of 2-oxoisovalerate dehydrogenase. This is the enzyme complex responsible for metabolism of pyruvate, 2-oxoglutarate, branched chain 2-oxo acids and acetoin. The E1 component is a heterotetramer of alpha2beta2. The homodimerised beta subunits are flanked by two alpha subunits in a 'vise' structure. [1]. 10426958. Crystal structure of 2-oxoisovalerate and dehydrogenase and the. architecture of 2-oxo acid dehydrogenase multienzyme complexes.. Aevarsson A, Seger K, Turley S, Sokatch JR, Hol WG;. Nat Struct Biol. 1999;6:785-792. (from Pfam)

Date:

2024-08-14

This domain is found on aromatic hydroxylating enzymes such as 2-oxo-1,2-dihydroquinoline 8-monooxygenase from Pseudomonas putida and carbazole 1,9a-dioxygenase from Janthinobacterium. These enzymes are homotrimers and are distantly related to the typical oxygenase [2]. This domain is found C terminal to the Rieske domain which binds an iron-sulphur cluster. [1]. 16005887. Structure of the terminal oxygenase component of angular. dioxygenase, carbazole 1,9a-dioxygenase.. Nojiri H, Ashikawa Y, Noguchi H, Nam JW, Urata M, Fujimoto Z,. Uchimura H, Terada T, Nakamura S, Shimizu K, Yoshida T, Habe H,. Omori T;. J Mol Biol. 2005;351:355-370.. [2]. 18922149. The Bet v 1 fold: an ancient, versatile scaffold for binding of. large, hydrophobic ligands.. Radauer C, Lackner P, Breiteneder H;. BMC Evol Biol. 2008;8:286. (from Pfam)

Date:

2024-08-14

EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) Pfam:PF01558 and the 4Fe-4S binding domain Fer4 Pfam:PF00037. It contains a characteristic EKR sequence motif. The exact function of this domain is not known. (from Pfam)

Date:

2024-08-14

MmlI is a short, approx 115 residue, protein of two alpha helices and four beta strands. It is involved in the catabolism of methyl-substituted aromatics via a modified oxo-adipate pathway in bacteria. The enzyme appears to be monomeric in some species [1] and tetrameric in others [2]. The known structure shows two copies of the protein form a dimeric alpha beta barrel. [1]. 2241929. Purification and characterization of 4-methylmuconolactone. methylisomerase, a novel enzyme of the modified 3-oxoadipate. pathway in the gram-negative bacterium Alcaligenes eutrophus JMP. 134.. Pieper DH, Stadler-Fritzsche K, Knackmuss HJ, Engesser KH, Bruce. NC, Cain RB;. Biochem J. 1990;271:529-534.. [2]. 2818569. Purification and characterization of 4-methylmuconolactone. methyl-isomerase, a novel enzyme of the modified 3-oxoadipate. pathway in nocardioform actinomycetes.. Bruce NC, Cain RB, Pieper DH, Engesser KH;. Biochem J. 1989;262:303-312. (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 includes mitochondrial D-glutamate cyclase which converts D-glutamate to 5-oxo-D-proline [1]. This family also includes numerous uncharacterised proteins from bacteria. [1]. 28266638. D-Glutamate is metabolized in the heart mitochondria.. Ariyoshi M, Katane M, Hamase K, Miyoshi Y, Nakane M, Hoshino A,. Okawa Y, Mita Y, Kaimoto S, Uchihashi M, Fukai K, Ono K,. Tateishi S, Hato D, Yamanaka R, Honda S, Fushimura Y, Iwai-Kanai. E, Ishihara N, Mita M, Homma H, Matoba S;. Sci Rep. 2017;7:43911. (from Pfam)

Date:

2024-08-14

This is the N-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain [1]. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity [2]. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK) [1]. [1]. 27402745. Assignment of function to a domain of unknown function: DUF1537. is a new kinase family in catabolic pathways for acid sugars.. Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S,. Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crecy-Lagard V,. Jacobson MP, Almo SC, Gerlt JA;. Proc Natl Acad Sci U S A. 2016;113:E4161-E4169.. [2]. 27294475. Members of a Novel Kinase Family (DUF1537) Can Recycle . TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain [1]. The communication domain is thought to play an important role in the heterodimerisation of the enzyme [1]. [1]. 12764229. Crystal structure of a bifunctional aldolase-dehydrogenase:. sequestering a reactive and volatile intermediate.. Manjasetty BA, Powlowski J, Vrielink A;. Proc Natl Acad Sci U S A 2003;100:6992-6997. (from Pfam)

Date:

2024-08-14

This family consists of several bacterial ethanolamine ammonia-lyase light chain (EutC) EC:4.3.1.7 sequences. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia [1]. [1]. 2197274. Cloning, sequencing, and expression of the genes encoding the. adenosylcobalamin-dependent ethanolamine ammonia-lyase of. Salmonella typhimurium.. Faust LR, Connor JA, Roof DM, Hoch JA, Babior BM;. J Biol Chem 1990;265:12462-12466. (from Pfam)

Date:

2024-08-14

Heterocyclic nitrogen compounds may serve as nitrogen sources or nitrogen transport compounds in plants that are not able to fix nitrogen. This family represents ureide permease, a transporter of a wide spectrum of oxo derivatives of heterocyclic nitrogen compounds, including allantoin, uric acid and xanthine; it has 10 putative transmembrane domains with a large cytosolic central domain containing a 'Walker A' motif. Ureide permease is likely to transport other purine degradation products when nitrogen sources are low. Transport is dependent on glucose and a proton gradient [1]. The family is found in bacteria, plants and yeast. These transporters are constituted of two sets of 5xTMs. [1]. 11971139. A novel superfamily of transporters for allantoin and other oxo. derivatives of nitrogen heterocyclic compounds in Arabidopsis.. Desimone M, Catoni E, Ludewig U, Hilpert M, Schneider A, Kunze. R, Tegeder M, Frommer WB, Schumacher K;. Plant Cell. 2002;14:847-856. (from Pfam)

Date:

2024-08-14

This family consists of several bacterial ethanolamine ammonia lyase large subunit (EutB) proteins (EC:4.3.1.7). Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. The enzyme is a heterodimer composed of subunits of Mr approximately 55,000 (EutB) and 35,000 (EutC) [1]. [1]. 2197274. Cloning, sequencing, and expression of the genes encoding the. adenosylcobalamin-dependent ethanolamine ammonia-lyase of. Salmonella typhimurium.. Faust LR, Connor JA, Roof DM, Hoch JA, Babior BM;. J Biol Chem 1990;265:12462-12466.. [2]. 10464203. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium. encodes five homologues of carboxysome shell proteins.. Kofoid E, Rappleye C, Stojiljkovic I, Roth J;. J Bacteriol 1999;181:5317-5329.. [3]. 8069783. Sequence of Rhodococcus gene cluster encoding the subunits of. ethanolamine ammonia-lyase and an APC-like permease.. De Mot R, Nagy I, Schoofs G, Vanderleyden J;. Can J Microbiol 1994;40:403-407. (from Pfam)

Gene:

eutB

Date:

2024-08-14

Members of this family belong to the PdxJ family that catalyses the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate [1]. [1]. 10225425. Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate. from 4-(phosphohydroxy)-L-threonine and. 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein.. Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS;. FEBS Lett 1999;449:45-48. (from Pfam)

Date:

2024-08-14

GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold. [1]. 7578111. Crystal structure of glycosomal glyceraldehyde-3-phosphate. dehydrogenase from Leishmania mexicana: implications for. structure-based drug design and a new position for the inorganic. phosphate binding site.. Kim H, Feil IK, Verlinde CL, Petra PH, Hol WG;. Biochemistry 1995;34:14975-14986. (from Pfam)

Date:

2024-08-14

This Pfam domain model identifies C-terminal domains of N-acetyl-glutamine semialdehyde dehydrogenase (AgrC), aspartate-semialdehyde dehydrogenase (Asd) and a few other, less common enzymes.

Date:

2024-08-14

Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This domain interacts with the tungsten cofactor [1]. [1]. 7878465. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde. ferredoxin oxidoreductase.. Chan MK, Mukund S, Kletzin A, Adams MW, Rees DC;. Science 1995;267:1463-1469. (from Pfam)

Date:

2024-08-14