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7  structures 709  species 0  interactions 974  sequences 12  architectures

Family: Peptidase_M54 (PF07998)

Summary: Peptidase family M54

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Peptidase family M54 Provide feedback

This is a family of metallopeptidases. Two human proteins have been reported to degrade synthetic substrates and peptides [1].

Literature references

  1. Diaz-Perales A, Quesada V, Peinado JR, Ugalde AP, Alvarez J, Suarez MF, Gomis-Ruth FX, Lopez-Otin C; , J Biol Chem. 2005;280:30367-30375.: Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea. PUBMED:15972818 EPMC:15972818

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012962

Peptidase family M54 (archaemetzincin or archaelysin) is a zinc-dependent aminopeptidase that contains the consensus zinc-binding sequence HEXXHXXGXXH/D and a conserved Met residue at the active site, and is thus classified as a metzincin. Archaemetzincins, first identified in archaea, are also found in bacteria and eukaryotes, including two human members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1 is mainly found in the liver and heart while AMZ2 is primarily expressed in testis and heart; both have been reported to be aminopeptidases, degrading synthetic substrates and peptides. The peptidase M54 family contains an extended metzincin concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that a second zinc ion is bound to four cysteines, thus resembling a zinc finger. Phylogenetic analysis of this family reveals a complex evolutionary process involving a series of lateral gene transfer, gene loss and genetic duplication events [ PUBMED:15972818 , PUBMED:20597090 , PUBMED:20561058 ].

Archaemetzincin (from Mycococcus xanthus) seem to have evolved into a zinc-binding transcription factor fulfilling only a structural role [ PUBMED:15972818 , PUBMED:20597090 , PUBMED:16879646 ]. The structure of archaemetzincin from Methanopyrus kandleri has been resolved [ PUBMED:20597090 ].

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.

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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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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_4509 (release 16.0)
Previous IDs: DUF1695;
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Bateman A
Number in seed: 5
Number in full: 974
Average length of the domain: 111.50 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 35.61 %

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 24.4 24.4
Trusted cut-off 24.4 24.4
Noise cut-off 24.3 24.3
Model length: 194
Family (HMM) version: 14
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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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_M54 domain has been found. There are 7 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
E7FFS8 View 3D Structure Click here
Q400C7 View 3D Structure Click here
Q400C8 View 3D Structure Click here
Q57729 View 3D Structure Click here
Q86W34 View 3D Structure Click here