Protein Family Models

This HMM describes a recurring sub-architecture, about 1500 amino acids long, with an SDR (short-chain alcohol reductase) at its C-terminus, in addition to a trio of domains shared by all type I polyketide synthases. While the actual function of member proteins is specific to the natural product made, this model is assigned family type equivalog_domain to elevate its precedence in automated annotation software and prevent the misapplication of even more generic annotation.

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2024-04-14

KAsynt_C_assoc represents the very C-terminus of a subset of proteins from the keto-acyl-synthetase 2 family. It is found in proteins ranging from bacteria to human. (from Pfam)

Date:

2023-12-12

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2023-12-12

This entry represents the N-terminal HotDog domain of the dehydratase (DH) module of polyketide synthases [1]. Structural analysis shows these DH domains are double hotdogs in which the active site contains a histidine from the N-terminal hotdog and an aspartate from the C-terminal hotdog. Studies have uncovered that a substrate tunnel formed between the DH domains may be essential for loading substrates and unloading products [2]. [1]. 18952099. Crystal structure of the erythromycin polyketide synthase. dehydratase.. Keatinge-Clay A;. J Mol Biol. 2008;384:941-953.. [2]. 20152156. Crystal structures of dehydratase domains from the curacin. polyketide biosynthetic pathway.. Akey DL, Razelun JR, Tehranisa J, Sherman DH, Gerwick WH, Smith. JL;. Structure. 2010;18:94-105. (from Pfam)

Date:

2024-04-03

This is the dimerisation element domain found in bacterial modular polyketide synthase ketoreductases [1]. The dimerization element (DE) domain is N-terminal to the KR domain Pfam:PF08659. DE domain is necessary for KR function, presumably because the dimeric DE orients the KR domains for optimal activity within a module [2]. [1]. 23489133. The missing linker: a dimerization motif located within. polyketide synthase modules.. Zheng J, Fage CD, Demeler B, Hoffman DW, Keatinge-Clay AT;. ACS Chem Biol. 2013;8:1263-1270.. [2]. 23755878. Structural studies of an A2-type modular polyketide synthase. ketoreductase reveal features controlling alpha-substituent. stereochemistry.. Zheng J, Piasecki SK, Keatinge-Clay AT;. ACS Chem Biol. 2013;8:1964-1971. (from Pfam)

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2024-04-03

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2023-12-12

This domain is found in Enoyl-(Acyl carrier protein) reductases. (from Pfam)

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2024-04-03

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2023-12-12

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:

2024-04-03

This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure [1-2]. [1]. 8804825. Structural classification of proteins: new superfamilies.. Murzin AG;. Curr Opin Struct Biol 1996;6:386-394.. [2]. 10556240. Conserved structural features and sequence patterns in the GroES. fold family.. Taneja B, Mande SC;. Protein Eng 1999;12:815-818. (from Pfam)

Date:

2024-04-03

This is a family of diverse bacterial polysaccharide biosynthesis proteins including the CapD protein (Swiss:P39853) [1], WalL protein (Swiss:O86159) mannosyl-transferase (Swiss:O05349) [2] and several putative epimerases (e.g. WbiI Swiss:O69130). [1]. 7961465. Sequence analysis and molecular characterization of genes. required for the biosynthesis of type 1 capsular polysaccharide. in Staphylococcus aureus.. Lin WS, Cunneen T, Lee CY;. J Bacteriol 1994;176:7005-7016.. [2]. 9079898. Identification of additional genes required for O-antigen. biosynthesis in Vibrio cholerae O1.. Fallarino A, Mavrangelos C, Stroeher UH, Manning PA;. J Bacteriol 1997;179:2147-2153. (from Pfam)

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2024-04-03

The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. [1]. 9482715. Crystal structure of beta-ketoacyl-acyl carrier protein synthase. II from E.coli reveals the molecular architecture of condensing. enzymes.. Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y;. EMBO J 1998;17:1183-1191. (from Pfam)

Date:

2024-04-03

This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions. [1]. 9174344. Structural analysis of UDP-sugar binding to UDP-galactose. 4-epimerase from Escherichia coli.. Thoden JB, Hegeman AD, Wesenberg G, Chapeau MC, Frey PA, Holden. HM;. Biochemistry 1997;36:6294-6304. (from Pfam)

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2024-04-03

Thiolase is reported to be structurally related to beta-ketoacyl synthase (Pfam:PF00109), and also chalcone synthase. [1]. 9402066. The 1.8 A crystal structure of the dimeric peroxisomal. 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae:. implications for substrate binding and reaction mechanism.. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A,. Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK;. J Mol Biol 1997;273:714-728. (from Pfam)

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2024-04-03

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2023-12-12

This family contains a wide variety of dehydrogenases. [1]. 9735295. The refined crystal structure of Drosophila lebanonensis alcohol. dehydrogenase at 1.9 A resolution.. Benach J, Atrian S, Gonzalez-Duarte R, Ladenstein R;. J Mol Biol 1998;282:383-399.. [2]. 10387002. Structure of tropinone reductase-II complexed with NADP+ and. pseudotropine at 1.9 A resolution: implication for. stereospecific substrate binding and catalysis.. Yamashita A, Kato H, Wakatsuki S, Tomizaki T, Nakatsu T,. Nakajima K, Hashimoto T, Yamada Y, Oda J;. Biochemistry 1999;38:7630-7637. (from Pfam)

Date:

2024-04-03

A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine. (from Pfam)

Date:

2023-12-12

The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine [1]. [1]. 9482715. Crystal structure of beta-ketoacyl-acyl carrier protein synthase. II from E.coli reveals the molecular architecture of condensing. enzymes.. Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y;. EMBO J 1998;17:1183-1191. (from Pfam)

Date:

2024-04-03

Date:

2023-12-12