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58  structures 5130  species 0  interactions 7174  sequences 42  architectures

Family: Peptidase_M17_N (PF02789)

Summary: Cytosol aminopeptidase family, N-terminal domain

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Cytosol aminopeptidase family, N-terminal domain Provide feedback

No Pfam abstract.

Literature references

  1. Burley SK, David PR, Taylor A, Lipscomb WN; , Proc Natl Acad Sci U S A 1990;87:6878-6882.: Molecular structure of leucine aminopeptidase at 2.7-A resolution. PUBMED:2395881 EPMC:2395881

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008283

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 M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine).

Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [ PUBMED:1555602 , PUBMED:2395881 ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids [ PUBMED:2395881 ].

The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another [ PUBMED:2395881 ]. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape [ PUBMED:2395881 ]. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices [ PUBMED:2395881 ]. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core [ PUBMED:2395881 ]. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer [ PUBMED:2395881 ]. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [ PUBMED:2395881 ].

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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Pfam Clan

This family is a member of clan MACRO (CL0223), which has the following description:

This superfamily includes the Macro domain as well as the amino terminal domain from peptidase M17 proteins.

The clan contains the following 8 members:

bCoV_SUD_M DUF2263 DUF2362 Macro Macro_2 PARG_cat Pdase_M17_N2 Peptidase_M17_N


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: Pfam-B_990 (release 3.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR
Number in seed: 68
Number in full: 7174
Average length of the domain: 123.6 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 24.76 %

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 23.4 23.4
Trusted cut-off 23.4 23.4
Noise cut-off 23.3 23.3
Model length: 126
Family (HMM) version: 20
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_M17_N domain has been found. There are 58 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
A0A077YZV7 View 3D Structure Click here
A0A077Z3I7 View 3D Structure Click here
A0A077ZNM5 View 3D Structure Click here
A0A0H3GLS3 View 3D Structure Click here
A0A1D6GRR2 View 3D Structure Click here
A0A1D6H8U7 View 3D Structure Click here
A0A1D6HN63 View 3D Structure Click here
A0KPF3 View 3D Structure Click here
A0LK12 View 3D Structure Click here
A0RUA5 View 3D Structure Click here
A1BGN2 View 3D Structure Click here
A1K9L5 View 3D Structure Click here
A1SRZ1 View 3D Structure Click here
A1UIA8 View 3D Structure Click here
A1VP99 View 3D Structure Click here
A1W776 View 3D Structure Click here
A1WSK3 View 3D Structure Click here
A1WUV1 View 3D Structure Click here
A1Z9G3 View 3D Structure Click here
A2BIC6 View 3D Structure Click here
A2SH61 View 3D Structure Click here
A3N1A7 View 3D Structure Click here
A3PEG6 View 3D Structure Click here
A3QBG2 View 3D Structure Click here
A4G7P5 View 3D Structure Click here
A4VNZ7 View 3D Structure Click here
A5G9C7 View 3D Structure Click here
A5GN62 View 3D Structure Click here
A5GV03 View 3D Structure Click here
A6THI2 View 3D Structure Click here
A6TWW9 View 3D Structure Click here
A6VMX3 View 3D Structure Click here
A6X259 View 3D Structure Click here
A7IFB7 View 3D Structure Click here
A8AMA5 View 3D Structure Click here
A8FH04 View 3D Structure Click here
A8ML24 View 3D Structure Click here
A9AHG9 View 3D Structure Click here
A9BBV5 View 3D Structure Click here
A9IIK3 View 3D Structure Click here