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491  structures 1743  species 0  interactions 12697  sequences 511  architectures

Family: Peptidase_M10 (PF00413)

Summary: Matrixin

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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.

Matrixin Provide feedback

The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.

Literature references

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

  2. Gooley PR, O'Connell JF, Marcy AI, Cuca GC, Salowe SP, Bush BL, Hermes JD, Esser CK, Hagmann WK, Springer JP, et al; , Nat Struct Biol 1994;1:111-118.: The NMR structure of the inhibited catalytic domain of human stromelysin-1. PUBMED:7656014 EPMC:7656014

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001818

Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site [ PUBMED:7674922 ]. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [ PUBMED:7674922 ].

This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)).

The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA.

Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [ PUBMED:2551898 , PUBMED:2167841 ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [ PUBMED:2841336 , PUBMED:1988438 ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [ PUBMED:2551898 , PUBMED:2167841 ].

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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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...

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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.

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

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Representative proteomes UniProt

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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.

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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...


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: Prosite
Previous IDs: matrixin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD
Number in seed: 67
Number in full: 12697
Average length of the domain: 163.60 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 34.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 159
Family (HMM) version: 27
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


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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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The tree shows the occurrence of this domain across different species. More...


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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 Peptidase_M10 domain has been found. There are 491 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
A0A0G2K5A5 View 3D Structure Click here
A0A0K3ARD1 View 3D Structure Click here
A0A0N9E2K8 View 3D Structure Click here
A0A0P0XXH3 View 3D Structure Click here
A0A0R0KRF2 View 3D Structure Click here
A0A0R0KW98 View 3D Structure Click here
A0A0R0KY07 View 3D Structure Click here
A0A0R0KYB1 View 3D Structure Click here
A0A0R4IB00 View 3D Structure Click here
A0A1D6HJU4 View 3D Structure Click here
A0A1D6K8F9 View 3D Structure Click here
A0A286Y9P6 View 3D Structure Click here
A0A286YB36 View 3D Structure Click here
A0A2R8Q2M8 View 3D Structure Click here
A0A2R8Q2R3 View 3D Structure Click here
A0A2R8RUJ1 View 3D Structure Click here
A0A368ULT7 View 3D Structure Click here
A1EC81 View 3D Structure Click here
B0R0I1 View 3D Structure Click here
B4FZU1 View 3D Structure Click here
B5DFD5 View 3D Structure Click here
C0M4B0 View 3D Structure Click here
C6TMH1 View 3D Structure Click here
D0EM77 View 3D Structure Click here
D3YV89 View 3D Structure Click here
D3ZCG5 View 3D Structure Click here
D3ZQ07 View 3D Structure Click here
D3ZRZ2 View 3D Structure Click here
D3ZXD9 View 3D Structure Click here
D3ZXJ0 View 3D Structure Click here
D3ZZ42 View 3D Structure Click here
E7F1N5 View 3D Structure Click here
E7F3C3 View 3D Structure Click here
E7F6P2 View 3D Structure Click here
E7FCZ5 View 3D Structure Click here
E7FFQ4 View 3D Structure Click here
E7FGL6 View 3D Structure Click here
E9QIX9 View 3D Structure Click here
F1Q899 View 3D Structure Click here
F1QBU4 View 3D Structure Click here