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1  structure 120  species 0  interactions 188  sequences 3  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

  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 140106Freely accessible. 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.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006765

Aromatic polyketides are assembled by a type II (iterative) polyketide synthases (PKSs) in bacteria. Type II PKS complexes consist of several monofunctional or bifunctional proteins which 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 [PUBMED:9224566, PUBMED:19903160].

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

Tetracenomycin F2 cyclase (TcmI) catalyses an aromatic rearrangement in the biosynthetic pathaway of tetracenomycin C from Streptomyces glaucescens. 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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Pfam Clan

This family is a member of clan Dim_A_B_barrel (CL0032), which has the following description:

This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel. The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases.

The clan contains the following 25 members:

ABM AsnC_trans_reg Chlor_dismutase Cyclase_polyket Dabb Dehydratase_hem DUF1330 DUF1428 DUF3291 DUF4188 DUF4242 DUF4937 Dyp_perox EthD GYD HapK MIase MmlI NapD NIPSNAP rhaM SchA_CurD SOR YCII ydhR

Alignments

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  Seed
(41)
Full
(188)
Representative proteomes UniProt
(555)
NCBI
(953)
Meta
(0)
RP15
(12)
RP35
(53)
RP55
(198)
RP75
(297)
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  Seed
(41)
Full
(188)
Representative proteomes UniProt
(555)
NCBI
(953)
Meta
(0)
RP15
(12)
RP35
(53)
RP55
(198)
RP75
(297)
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  Seed
(41)
Full
(188)
Representative proteomes UniProt
(555)
NCBI
(953)
Meta
(0)
RP15
(12)
RP35
(53)
RP55
(198)
RP75
(297)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_5596 (release 7.5)
Previous IDs: cyclase_polyket;
Type: Domain
Author: Mifsud W
Number in seed: 41
Number in full: 188
Average length of the domain: 102.80 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 91.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.4 24.4
Trusted cut-off 24.4 25.0
Noise cut-off 24.2 23.0
Model length: 104
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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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