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0  structures 575  species 0  interactions 1197  sequences 9  architectures

Family: Abhydrolase_4 (PF08386)

Summary: TAP-like protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Alpha/beta hydrolase fold". More...

Alpha/beta hydrolase fold Edit Wikipedia article

1qge opm.gif
A bacterial lipase, one of this family members
Identifiers
Symbol Abhydrolase_1
Pfam PF00561
InterPro IPR000073
SCOP 1ede
SUPERFAMILY 1ede
OPM superfamily 135
OPM protein 1qge

In molecular biology, the alpha/beta hydrolase fold is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function.[1] The core of each enzyme is an alpha/beta-sheet (rather than a barrel), containing 8 beta strands connected by 6 alpha helices.[1][2] The enzymes are believed to have diverged from a common ancestor, preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best-conserved structural features of the fold.

This catalytic domain is found in a very wide range of enzymes which do not share obvious sequence similarity. The alpha/beta hydrolase fold includes proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases.[3]

Database[edit]

The ESTHER database provides a large collection of information about this family of proteins.[4]

Subfamilies[edit]

Human proteins containing this domain[edit]

ABHD10; ABHD11; ABHD12; ABHD12B; ABHD13; ABHD2; ABHD3; ABHD4; ABHD5; ABHD6; ABHD7; ABHD8; ABHD9; BAT5; BPHL; C20orf135; EPHX1; EPHX2; FAM108B1; LIPA; LIPF; LIPJ; LIPK; LIPM; LIPN; MEST; MGLL; PPME1; SERHL; SERHL2; SPG21; CES1; CES2

See also[edit]

  • Serine hydrolase - an enzyme family that is composed largely of proteins with alpha-beta hydrolase folds

External links[edit]

References[edit]

  1. ^ a b Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schrag, J., Sussman, J. L., Verschueren, K. H. G. & Goldman, A. (1992). "The alpha/beta hydrolase fold". Protein Eng. 5 (3): 197–211. doi:10.1093/protein/5.3.197. PMID 1409539. 
  2. ^ Carr PD, Ollis DL (2009). "Alpha/beta hydrolase fold: an update". Protein Pept. Lett. 16 (10): 1137–48. PMID 19508187. 
  3. ^ Nardini M, Dijkstra BW (December 1999). "Alpha/beta hydrolase fold enzymes: the family keeps growing". Curr. Opin. Struct. Biol. 9 (6): 732–7. doi:10.1016/S0959-440X(99)00037-8. PMID 10607665. 
  4. ^ Renault L, Nègre V, Hotelier T, Cousin X, Marchot P, Chatonnet A (December 2005). "New friendly tools for users of ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins". Chem. Biol. Interact. 157-158: 339–43. doi:10.1016/j.cbi.2005.10.100. PMID 16297901. 

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

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.

TAP-like protein Provide feedback

This is a family of putative bacterial peptidases and hydrolases that bear similarity to a tripeptidyl aminopeptidase isolated from Streptomyces lividans (Q54410). A member of this family (Q6E3K7) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii [1].

Literature references

  1. Brede DA, Faye T, Johnsborg O, Odegard I, Nes IF, Holo H; , Appl Environ Microbiol 2004;70:7303-7310.: Molecular and genetic characterization of propionicin F, a bacteriocin from Propionibacterium freudenreichii. PUBMED:15574930 EPMC:15574930


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013595

In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:

  • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
  • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.

In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [PUBMED:7845208]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence [PUBMED:7845208]. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [PUBMED:7845208].

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [PUBMED:7845208]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds [PUBMED:7845208]. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [PUBMED:7845208, PUBMED:8439290].

This entry represents a C-terminal domain associated with putative hydrolases and bacterial peptidases that belong to MEROPS peptidase family S33 (clan SC). They are related to a tripeptidyl aminopeptidase from Streptomyces lividans (SWISSPROT). A member of this family (SWISSPROT) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii [PUBMED:15574930].

Gene Ontology

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

Domain organisation

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

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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
(38)
Full
(1197)
Representative proteomes NCBI
(3862)
Meta
(878)
RP15
(153)
RP35
(319)
RP55
(425)
RP75
(480)
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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, x not generated, not available.

Format an alignment

  Seed
(38)
Full
(1197)
Representative proteomes NCBI
(3862)
Meta
(878)
RP15
(153)
RP35
(319)
RP55
(425)
RP75
(480)
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
(38)
Full
(1197)
Representative proteomes NCBI
(3862)
Meta
(878)
RP15
(153)
RP35
(319)
RP55
(425)
RP75
(480)
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_3096 (release 18.0)
Previous IDs: none
Type: Family
Author: Fenech M
Number in seed: 38
Number in full: 1197
Average length of the domain: 102.40 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 19.93 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 103
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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