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Items: 1 to 20 of 44

1.

KR prefix domain-containing protein

This domain appears as an N-terminal sub-domain in some forms of KR (keto-reductase) domain found in polyketide reductases.

Date:
2024-12-16
Family Accession:
NF047870.1
Method:
HMM
2.

Polyketide synthase dehydratase domain

This domain is part of a dehydratase domain found in diverse PKS enzymes. This domain adopts a HotDog fold. Paper describing PDB structure 2vz8. [1]. 18772430. The crystal structure of a mammalian fatty acid synthase. Maier T, Leibundgut M, Ban N;. Science. 2008;321:1315-1322. Paper describing PDB structure 3el6. [2]. 18952099. Crystal structure of the erythromycin polyketide synthase dehydratase. Keatinge-Clay A;. J Mol Biol. 2008;384:941-953. Paper describing PDB structure 3hhd. [3]. 20132826. Structure of the human fatty acid synthase KS-MAT didomain as a framework for inhibitor design. Pappenberger G, Benz J, Gsell B, Hennig M, Ruf A, Stihle M, Thoma R, Rudolph MG;. J Mol Biol. 2010;397:508-519. Paper describing PDB structure 3hrq. [4]. 19847268. Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization. Crawford JM, Korman TP, Labonte JW, Vagstad AL, Hill EA, Kamari-Bidkorpeh O, Tsai SC, Townsend CA;. Nature. 2009;461:1139-1143. Paper describing PDB structure 3kg6. [5]. 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:
2024-10-16
Family Accession:
NF044701.2
Method:
HMM
3.

ketoacyl-synthetase C-terminal extension domain-containing protein

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:
2024-08-14
Family Accession:
NF027522.5
Method:
HMM
4.

CurL-like, PKS C-terminal

This entry represents the polyketide synthase C-terminal extension from cyanobacterial CurL polyketide synthase and similar proteins from other bacteria and fungi [1-5]. Paper describing PDB structure 2hg4. [1]. 16844787. The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase. Tang Y, Kim CY, Mathews II, Cane DE, Khosla C;. Proc Natl Acad Sci U S A. 2006;103:11124-11129. Paper describing PDB structure 2qo3. [2]. 17719492. Structural and mechanistic analysis of protein interactions in module 3 of the 6-deoxyerythronolide B synthase. Tang Y, Chen AY, Kim CY, Cane DE, Khosla C;. Chem Biol. 2007;14:931-943. Paper describing PDB structure 4kc5. [3]. 24048471. Vinylogous chain branching catalysed by a dedicated polyketide synthase module. Bretschneider T, Heim JB, Heine D, Winkler R, Busch B, Kusebauch B, Stehle T, Zocher G, Hertweck C;. Nature. 2013;502:124-128. Paper describing PDB structure 4mz0. [4]. 24183970. Cyanobacterial polyketide synthase docking domains: a tool for engineering natural product biosynthesis. Whicher JR, Smaga SS, Hansen DA, Brown WC, Gerwick WH, Sherman DH, Smith JL;. Chem Biol. 2013;20:1340-1351. Paper describing PDB structure 4na1. [5]. 24508341. A close look at a ketosynthase from a trans-acyltransferase modular polyketide synthase. Gay DC, Gay G, Axelrod AJ, Jenner M, Kohlhaas C, Kampa A, Oldham NJ, Piel J, Keatinge-Clay AT;. Structure. 2014;22:444-451. (from Pfam)

Date:
2024-10-16
Family Accession:
NF046877.1
Method:
HMM
5.

RhiE-like, KS-MAT linker domain

This entry represents a linker domain found in polyketide synthases, which connects the N-terminal domains with the B-domain as described in RhiE [1-3]. Paper describing PDB structure 4kc5. [1]. 24048471. Vinylogous chain branching catalysed by a dedicated polyketide synthase module. Bretschneider T, Heim JB, Heine D, Winkler R, Busch B, Kusebauch B, Stehle T, Zocher G, Hertweck C;. Nature. 2013;502:124-128. Paper describing PDB structure 4na1. [2]. 24508341. A close look at a ketosynthase from a trans-acyltransferase modular polyketide synthase. Gay DC, Gay G, Axelrod AJ, Jenner M, Kohlhaas C, Kampa A, Oldham NJ, Piel J, Keatinge-Clay AT;. Structure. 2014;22:444-451. Paper describing PDB structure 4tkt. [3]. 26420866. Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases. Lohman JR, Ma M, Osipiuk J, Nocek B, Kim Y, Chang C, Cuff M, Mack J, Bigelow L, Li H, Endres M, Babnigg G, Joachimiak A, Phillips GN Jr, Shen B;. Proc Natl Acad Sci U S A. 2015;112:12693-12698. Paper describing PDB structure 5e5n. [4]. 26724270. The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex. Gay DC, Wagner DT, Meinke JL, Zogzas CE, Gay GR, Keatinge-Clay AT;. J Struct Biol. 2016;193:196-205. (from Pfam)

Date:
2024-10-16
Family Accession:
NF046639.1
Method:
HMM
6.

Beta-ketoacyl synthase-like, N-terminal

This is the N-terminal adenylation (A) domain of bacterial beta-ketoacyl synthases [1]. This domain selects the alpha-keto acid that then adenylates and transfer to the PCP domain. Paper describing PDB structure 6ulw. [1]. 32066969. Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis. Alonzo DA, Chiche-Lapierre C, Tarry MJ, Wang J, Schmeing TM;. Nat Chem Biol. 2020;16:493-496. (from Pfam)

Date:
2024-10-16
Family Accession:
NF045055.2
Method:
HMM
7.

polyketide synthase dehydratase domain-containing protein

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:
2024-10-16
Family Accession:
NF026115.5
Method:
HMM
8.

zinc-binding dehydrogenase

Date:
2024-08-14
Family Accession:
NF024989.5
Method:
HMM
9.

KR domain-containing protein

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:
2024-10-16
Family Accession:
NF020243.5
Method:
HMM
10.

alcohol dehydrogenase catalytic domain-containing protein

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:
2024-10-16
Family Accession:
NF019845.5
Method:
HMM
11.

Beta-ketoacyl synthase, C-terminal domain

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:
2024-10-16
Family Accession:
NF014819.5
Method:
HMM
12.

phosphopantetheine-binding protein

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:
2024-08-14
Family Accession:
NF012759.5
Method:
HMM
13.

SDR family NAD(P)-dependent oxidoreductase

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:
2024-10-16
Family Accession:
NF012334.5
Method:
HMM
14.

AMP-binding protein

Date:
2024-08-14
Family Accession:
NF012711.5
Method:
HMM
15.

beta-ketoacyl synthase N-terminal-like domain-containing protein

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:
2024-10-16
Family Accession:
NF012337.5
Method:
HMM
16.

zinc-binding dehydrogenase

Date:
2024-08-14
Family Accession:
NF012335.5
Method:
HMM
17.

acyltransferase domain-containing protein

Date:
2024-08-14
Family Accession:
NF012901.5
Method:
HMM
18.
new record, indexing in progress
Family Accession:
19.
new record, indexing in progress
Family Accession:
20.
new record, indexing in progress
Family Accession:

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