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90  structures 2042  species 1  interaction 8297  sequences 30  architectures

Family: CoA_transf_3 (PF02515)

Summary: CoA-transferase family III

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CoA-transferase family III Provide feedback

CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.

Literature references

  1. Heider J; , FEBS Lett 2001;509:345-349.: A new family of CoA-transferases. PUBMED:11749953 EPMC:11749953


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003673

CoA-transferases are found in organisms from all kingdoms of life. They catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids. There are at least three families of CoA-transferases, which differ in sequence and reaction mechanism:

  • Family I consists of CoA-transferases for 3-oxoacids (EC, EC), short-chain fatty acids (EC, EC) and glutaconate (EC). Most use succinyl-CoA or acetyl-CoA as CoA donors.
  • Family II consists of the homodimeric alpha-subunits of citrate lyase and citramalate lyase (EC, EC). These enzymes catalyse the transfer of acyl carrier protein (ACP) with a covalently bound CoA derivative, but can accept free CoA thioesters as well.
  • Family III consists of formyl-CoA:oxalate CoA-transferase [PUBMED:15213226], succinyl-CoA:(R)-benzylsuccinate CoA-transferase [PUBMED:11418570], (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase [PUBMED:10849007], and butyrobetainyl-CoA:(R)-carnitine CoA-transferase [PUBMED:15823031]. These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate- and stereo-specific manner [PUBMED:11749953].
This entry represents family III CoA-transferases.

Gene Ontology

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Domain organisation

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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
(118)
Full
(8297)
Representative proteomes NCBI
(7416)
Meta
(4895)
RP15
(656)
RP35
(1710)
RP55
(2447)
RP75
(3017)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(118)
Full
(8297)
Representative proteomes NCBI
(7416)
Meta
(4895)
RP15
(656)
RP35
(1710)
RP55
(2447)
RP75
(3017)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(118)
Full
(8297)
Representative proteomes NCBI
(7416)
Meta
(4895)
RP15
(656)
RP35
(1710)
RP55
(2447)
RP75
(3017)
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.

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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

Note: You can also download the data file for the tree.

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_887 (release 5.4)
Previous IDs: CAIB-BAIF;
Type: Family
Author: Mian N, Bateman A, Heider J
Number in seed: 118
Number in full: 8297
Average length of the domain: 185.50 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 47.03 %

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 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.5 20.4
Model length: 191
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

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

CoA_transf_3

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 CoA_transf_3 domain has been found. There are 90 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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