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1  structure 90  species 1  interaction 122  sequences 2  architectures

Family: Cyclase_polyket (PF04673)

Summary: Polyketide synthesis cyclase

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This is the Wikipedia entry entitled "Polyketide synthesis cyclase family". More...

Polyketide synthesis cyclase family Edit Wikipedia article

Cyclase_polyket
PDB 1tuw EBI.jpg
structural and functional analysis of tetracenomycin f2 cyclase from streptomyces glaucescens: a type-ii polyketide cyclase
Identifiers
Symbol Cyclase_polyket
Pfam PF04673
InterPro IPR006765

In molecular biology, the polyketide synthesis cyclase family of proteins includes a number of cyclases involved in polyketide synthesis in a number of actinobacterial species.

Aromatic polyketides are assembled by a type II (iterative) polyketide synthase in bacteria. Iterative type II polyketide synthases produce polyketide chains of variable but defined length from a specific starter unit and a number of extender units. They also specify the initial regiospecific folding and cyclisation pattern of nascent polyketides either through the action of a cyclase (CYC) subunit or through the combined action of site-specific ketoreductase and CYC subunits. Additional CYCs and other modifications may be necessary to produce linear aromatic polyketides.

The Tetracenomycin polyketide synthesis protein, tcmI, from Streptomyces glaucescens catalyses an aromatic rearrangement in the biosynthetic pathaway of tetracenomycin C from Streptomyces coelicolor. The protein is a homodimer where each subunit forms a beta-alpha-beta fold belonging to the ferrodoxin fold superfamily.[1] Four strands of antiparallel sheets and a layer of alpha helices create a cavity which was proposed to be the active site. This structure shows strong topological similarity to a polyketide monoxygenase from Streptomyces coelicolor which functions in the actinorhodin biosynthesic pathway.[2] It was suggested, therefore, that this fold is well suited to serve as a framework for rearrangements and chemical modification of polyaromatic substrates.

References[edit]

  1. ^ Thompson TB, Katayama K, Watanabe K, Hutchinson CR, Rayment I (September 2004). "Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase". J. Biol. Chem. 279 (36): 37956–63. doi:10.1074/jbc.M406144200. PMID 15231835. 
  2. ^ Sciara G, Kendrew SG, Miele AE, Marsh NG, Federici L, Malatesta F, Schimperna G, Savino C, Vallone B (January 2003). "The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis". EMBO J. 22 (2): 205–15. doi:10.1093/emboj/cdg031. PMC 140106. PMID 12514126. 

This article incorporates text from the public domain Pfam and InterPro IPR006765

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Polyketide synthesis cyclase Provide feedback

This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006765

Aromatic polyketides are assembled by a type II (iterative) polyketide synthase in bacteria. Iterative type II polyketide synthases produce polyketide chains of variable but defined length from a specific starter unit and a number of extender units. They also specify the initial regiospecific folding and cyclization pattern of nascent polyketides either through the action of a cyclase (CYC) subunit or through the combined action of site-specific ketoreductase and CYC subunits. Additional CYCs and other modifications may be necessary to produce linear aromatic polyketides.

This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species.

TcmI (SWISSPROT) catalyses an aromatic rearrangement in the biosynthetic pathaway of tetracenomycin C from Streptomyces coelicolor. The protein is a homodimer where each subunit forms a beta-alpha-beta fold belonging to the ferrodoxin fold superfamily [PUBMED:15231835]. Four strands of antiparallel sheets and a layer of alpha helices create a cavity which was proposed to be the active site. This structure shows strong topological similarity to a polyketide monoxygenase (SWISSPROT) from S. coelicolor which functions in the actinorhodin biosynthesic pathway [PUBMED:12514126]. It was suggested, therefore, that this fold is well suited to serve as a framework for rearrangements and chemical modification of polyaromatic substrates.

Gene Ontology

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Domain organisation

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  Seed
(23)
Full
(122)
Representative proteomes NCBI
(120)
Meta
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RP15
(10)
RP35
(30)
RP55
(38)
RP75
(40)
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  Seed
(23)
Full
(122)
Representative proteomes NCBI
(120)
Meta
(0)
RP15
(10)
RP35
(30)
RP55
(38)
RP75
(40)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Curation and family details

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Seed source: Pfam-B_5596 (release 7.5)
Previous IDs: cyclase_polyket;
Type: Family
Author: Mifsud W
Number in seed: 23
Number in full: 122
Average length of the domain: 96.20 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 87.19 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.7 23.7
Trusted cut-off 25.0 53.0
Noise cut-off 23.3 23.6
Model length: 97
Family (HMM) version: 7
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Species distribution

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Interactions

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Cyclase_polyket

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Cyclase_polyket domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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