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10  structures 888  species 1  interaction 1320  sequences 4  architectures

Family: Acyl_CoA_thio (PF02551)

Summary: Acyl-CoA thioesterase

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Acyl-CoA thioesterase Provide feedback

This family represents the thioesterase II domain. Two copies of this domain are found in a number of acyl-CoA thioesterases.

Literature references

  1. Watanabe H, Shiratori T, Shoji H, Miyatake S, Okazaki Y, Ikuta K, Sato T, Saito T; , Biochem Biophys Res Commun 1997;238:234-239.: A novel acyl-CoA thioesterase enhances its enzymatic activity by direct binding with HIV Nef. PUBMED:9299485 EPMC:9299485

  2. Naggert J, Narasimhan ML, DeVeaux L, Cho H, Randhawa ZI, Cronan JE Jr, Green BN, Smith S; , J Biol Chem 1991;266:11044-11050.: Cloning, sequencing, and characterization of Escherichia coli thioesterase II. PUBMED:1645722 EPMC:1645722


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025652

Escherichia coli thioesterase II reveals a new tertiary fold: a 'double hot dog'. It has an internal repeat with a basic unit that is structurally similar to the recently described beta-hydroxydecanoyl thiol ester dehydrase [PUBMED:10876240].

This entry represents the thioesterase II domain. Two copies of this domain are found in a number of acyl-CoA thioesterases.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HotDog (CL0050), which has the following description:

The HotDog fold was first observed in the structure of Escherichia coli beta-hydroxydecanoyl thiol ester dehydratase (FabA), where Leesong et al. noticed that each subunit of this dimeric enzyme contained a mixed alpha + beta 'hot dog' fold. They described the seven-stranded antiparallel beta-sheet as the 'bun', which wraps around a five-turn alpha-helical 'sausage', This superfamily contains a diverse range of enzymes. Membership includes numerous prokaryotic, archaeal and eukaryotic proteins involved in several related, but distinct, catalytic activities, from metabolic roles such as thioester hydrolysis in fatty acid metabolism, to degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. The superfamily also includes FapR, a non-catalytic bacterial homologue that is involved in transcriptional regulation of fatty acid biosynthesis [1].

The clan contains the following 13 members:

4HBT 4HBT_2 4HBT_3 Acyl-ACP_TE Acyl_CoA_thio AfsA DUF4442 FabA FcoT MaoC_dehydrat_N MaoC_dehydratas PS-DH YiiD_Cterm

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
(9)
Full
(1320)
Representative proteomes NCBI
(2384)
Meta
(900)
RP15
(28)
RP35
(69)
RP55
(120)
RP75
(170)
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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
(9)
Full
(1320)
Representative proteomes NCBI
(2384)
Meta
(900)
RP15
(28)
RP35
(69)
RP55
(120)
RP75
(170)
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
(9)
Full
(1320)
Representative proteomes NCBI
(2384)
Meta
(900)
RP15
(28)
RP35
(69)
RP55
(120)
RP75
(170)
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: SCOP
Previous IDs: none
Type: Domain
Author: Bashton M, Bateman A, Griffiths-Jones SR
Number in seed: 9
Number in full: 1320
Average length of the domain: 124.10 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 59.06 %

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 21.2 20.7
Noise cut-off 20.6 20.5
Model length: 132
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

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

Acyl_CoA_thio

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 Acyl_CoA_thio domain has been found. There are 10 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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