Summary: Polyketide synthesis cyclase

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Wikipedia: Polyketide synthesis cyclase family
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Polyketide synthesis cyclase family Edit Wikipedia article

Cyclase_polyket

structural and functional analysis of tetracenomycin f2 cyclase from streptomyces glaucescens: a type-ii polyketide cyclase

Identifiers

Symbol

Cyclase_polyket

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

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.

[edit] References

^ 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): 3795663. doi:10.1074/jbc.M406144200. PMID 15231835.
^ 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): 20515. doi:10.1093/emboj/cdg031. PMC 140106. PMID 12514126. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=140106.

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

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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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

PANDIT:	PF04673
Pseudofam:	PF04673
SYSTERS:	Cyclase_polyket

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

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Biological process

polyketide biosynthetic process (GO:0030639)

Domain organisation

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Alignments

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There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (23)	Full (122)	Representative proteomes				NCBI (120)	Meta (0)
	Seed (23)	Full (122)	RP15 (10)	RP35 (30)	RP55 (38)	RP75 (40)	NCBI (120)	Meta (0)
Jalview	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (23)	Full (122)	Representative proteomes				NCBI (120)	Meta (0)
	Seed (23)	Full (122)	RP15 (10)	RP35 (30)	RP55 (38)	RP75 (40)	NCBI (120)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (23)	Full (122)	Representative proteomes				NCBI (120)	Meta (0)
	Seed (23)	Full (122)	RP15 (10)	RP35 (30)	RP55 (38)	RP75 (40)	NCBI (120)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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

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

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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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

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Species trees

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Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

There is 1 interaction for this family. More...

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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Cyclase_polyket (PF04673)

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Summary: Polyketide synthesis cyclase

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Polyketide synthesis cyclase family Edit Wikipedia article

[edit] References

Polyketide synthesis cyclase Provide feedback

External database links

InterPro entry IPR006765

Gene Ontology

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures