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156  structures 8662  species 0  interactions 61690  sequences 292  architectures

Family: M20_dimer (PF07687)

Summary: Peptidase dimerisation domain

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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.

Peptidase dimerisation domain Provide feedback

This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the M20 family of peptidases [1]. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification [2]. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases.

Literature references

  1. Rowsell S, Pauptit RA, Tucker AD, Melton RG, Blow DM, Brick P; , Structure 1997;5:337-347.: Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy. PUBMED:9083113 EPMC:9083113

  2. Rawlings ND, Barrett AJ; , Meth Enzymol 1995;248:183-228.: Evolutionary families of metallopeptidases. PUBMED:7674922 EPMC:7674922


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011650

This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the MEROPS peptidase family M20 [ PUBMED:9083113 ]. This family includes a range of zinc exopeptidases: carboxypeptidases, dipeptidases and specialised aminopeptidases [ PUBMED:7674922 ].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(175)
Full
(61690)
Representative proteomes UniProt
(262588)
RP15
(6926)
RP35
(27866)
RP55
(60843)
RP75
(105193)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(175)
Full
(61690)
Representative proteomes UniProt
(262588)
RP15
(6926)
RP35
(27866)
RP55
(60843)
RP75
(105193)
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
(175)
Full
(61690)
Representative proteomes UniProt
(262588)
RP15
(6926)
RP35
(27866)
RP55
(60843)
RP75
(105193)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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.

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_253 (release 4.0)
Previous IDs: Peptidase_M20;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Studholme DJ
Number in seed: 175
Number in full: 61690
Average length of the domain: 116.90 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 27.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -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: 109
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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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 M20_dimer domain has been found. There are 156 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0XI05 View 3D Structure Click here
A0A0R0GUR9 View 3D Structure Click here
A0A0R0IPJ5 View 3D Structure Click here
A0A0R0IPM0 View 3D Structure Click here
A0A0R0IPU2 View 3D Structure Click here
A0A0R0IYN4 View 3D Structure Click here
A0A0R4J3Y3 View 3D Structure Click here
A0A0R4J5T7 View 3D Structure Click here
A0A1D6KJ07 View 3D Structure Click here
A0A1D8PDN2 View 3D Structure Click here
A0A1D8PIK3 View 3D Structure Click here
A0A1D8PLD9 View 3D Structure Click here
A0A1D8PLQ3 View 3D Structure Click here
A0A381MQ29 View 3D Structure Click here
A0KIB5 View 3D Structure Click here
A0KIP7 View 3D Structure Click here
A0L3N2 View 3D Structure Click here
A0Q3I1 View 3D Structure Click here
A0R2G4 View 3D Structure Click here
A1AVU9 View 3D Structure Click here
A1B5Y2 View 3D Structure Click here
A1CAX3 View 3D Structure Click here
A1CE70 View 3D Structure Click here
A1DM79 View 3D Structure Click here
A1K719 View 3D Structure Click here
A1S647 View 3D Structure Click here
A1SXF9 View 3D Structure Click here
A1TQ19 View 3D Structure Click here
A1UUD2 View 3D Structure Click here
A1VN92 View 3D Structure Click here
A1W7M0 View 3D Structure Click here
A1WEL1 View 3D Structure Click here
A1WX26 View 3D Structure Click here
A2RBC2 View 3D Structure Click here
A2SGS4 View 3D Structure Click here
A3CNH0 View 3D Structure Click here
A3CQT4 View 3D Structure Click here
A3KG59 View 3D Structure Click here
A3KQX1 View 3D Structure Click here
A3N3G9 View 3D Structure Click here