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321  structures 6520  species 0  interactions 27464  sequences 381  architectures

Family: Peptidase_M1 (PF01433)

Summary: Peptidase family M1 domain

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Peptidase family M1 domain Provide feedback

Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues. This family includes leukotriene-A4 hydrolase P09960 this enzyme also has an aminopeptidase activity [1].

Literature references

  1. 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 IPR014782

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 M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA.

Membrane alanine aminopeptidase ( EC ) is part of the HEXXH + E group; it consists entirely of aminopeptidases, spread across a wide variety of species [ PUBMED:7674922 ]. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator [ PUBMED:7674922 ]. This hydrolase has been shown to have aminopeptidase activity [ PUBMED:2244921 ], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [ PUBMED:7674922 ] CD13 participates in trimming peptides bound to MHC class II molecules [ PUBMED:8691132 ] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils [ PUBMED:8627182 ]. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory tract infections.

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 (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
(23)
Full
(27464)
Representative proteomes UniProt
(85258)
RP15
(4169)
RP35
(11829)
RP55
(25824)
RP75
(40915)
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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
(23)
Full
(27464)
Representative proteomes UniProt
(85258)
RP15
(4169)
RP35
(11829)
RP55
(25824)
RP75
(40915)
Alignment:
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Sequence:
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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
(23)
Full
(27464)
Representative proteomes UniProt
(85258)
RP15
(4169)
RP35
(11829)
RP55
(25824)
RP75
(40915)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Swiss-Prot
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 23
Number in full: 27464
Average length of the domain: 201.30 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 26.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.7 27.7
Trusted cut-off 27.7 27.7
Noise cut-off 27.6 27.6
Model length: 218
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 Peptidase_M1 domain has been found. There are 321 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
A0A0B4KH77 View 3D Structure Click here
A0A0R0IPA5 View 3D Structure Click here
A0A0R0J526 View 3D Structure Click here
A0A0R0K5H8 View 3D Structure Click here
A0A0R4ICL9 View 3D Structure Click here
A0A0R4INQ5 View 3D Structure Click here
A0A0R4IZV6 View 3D Structure Click here
A0A1D6EU67 View 3D Structure Click here
A0A1D6EU68 View 3D Structure Click here
A0A1D6G842 View 3D Structure Click here
A0A1D6H703 View 3D Structure Click here
A0A1D6HC35 View 3D Structure Click here
A0A1D6HP76 View 3D Structure Click here
A0A1D6HQ98 View 3D Structure Click here
A0A1D6I2Y6 View 3D Structure Click here
A0A1D6KM22 View 3D Structure Click here
A0A1D6KPN1 View 3D Structure Click here
A0A1D6LSN9 View 3D Structure Click here
A0A1D6NK55 View 3D Structure Click here
A0A1D6PEP0 View 3D Structure Click here
A0A1D6QRS6 View 3D Structure Click here
A0A1D8PQC4 View 3D Structure Click here
A0A286YAT8 View 3D Structure Click here
A0A2R8Q716 View 3D Structure Click here
A0A2R8QBK0 View 3D Structure Click here
A0A2R8RIM7 View 3D Structure Click here
A0A2R8RTV8 View 3D Structure Click here
A2BGR0 View 3D Structure Click here
A4I4T3 View 3D Structure Click here
A4I709 View 3D Structure Click here
A5A631 View 3D Structure Click here
A5PMQ1 View 3D Structure Click here
A6NEC2 View 3D Structure Click here
B0V1A5 View 3D Structure Click here
B7EA73 View 3D Structure Click here
B8JIB4 View 3D Structure Click here
C0P5E7 View 3D Structure Click here
C7G081 View 3D Structure Click here
D3ZZW8 View 3D Structure Click here
E7F123 View 3D Structure Click here
E7F2N2 View 3D Structure Click here
E7FA17 View 3D Structure Click here
E9AGI7 View 3D Structure Click here
E9AHB1 View 3D Structure Click here
E9QIR0 View 3D Structure Click here
F1M9V7 View 3D Structure Click here
F1Q5Y3 View 3D Structure Click here
F1QRM9 View 3D Structure Click here
G5E872 View 3D Structure Click here
G5EFT4 View 3D Structure Click here
G5EGH4 View 3D Structure Click here
H2L0M5 View 3D Structure Click here
I1JTZ0 View 3D Structure Click here
I1K8E3 View 3D Structure Click here
I1MUG4 View 3D Structure Click here
I1NJ89 View 3D Structure Click here
K7KNH3 View 3D Structure Click here
K7MHA2 View 3D Structure Click here
L7N655 View 3D Structure Click here
M0RA44 View 3D Structure Click here
O09175 View 3D Structure Click here
O44183 View 3D Structure Click here
O94544 View 3D Structure Click here
P04825 View 3D Structure Click here
P09960 View 3D Structure Click here
P15144 View 3D Structure Click here
P15684 View 3D Structure Click here
P16406 View 3D Structure Click here
P24527 View 3D Structure Click here
P30349 View 3D Structure Click here
P32454 View 3D Structure Click here
P37898 View 3D Structure Click here
P40462 View 3D Structure Click here
P50123 View 3D Structure Click here
P52922 View 3D Structure Click here
P55786 View 3D Structure Click here
P69527 View 3D Structure Click here
P97449 View 3D Structure Click here
P97629 View 3D Structure Click here
Q07075 View 3D Structure Click here
Q0J2B5 View 3D Structure Click here
Q0J5V5 View 3D Structure Click here
Q0KI00 View 3D Structure Click here
Q0KI25 View 3D Structure Click here
Q10740 View 3D Structure Click here
Q10836 View 3D Structure Click here
Q11011 View 3D Structure Click here
Q17405 View 3D Structure Click here
Q22317 View 3D Structure Click here
Q22531 View 3D Structure Click here
Q22531 View 3D Structure Click here
Q24325 View 3D Structure Click here
Q2KHK3 View 3D Structure Click here
Q4CTQ4 View 3D Structure Click here
Q4CXX8 View 3D Structure Click here
Q4D5P1 View 3D Structure Click here
Q4DAN8 View 3D Structure Click here
Q4DLT0 View 3D Structure Click here
Q4DMV3 View 3D Structure Click here
Q4E5S1 View 3D Structure Click here
Q4E686 View 3D Structure Click here
Q4TT88 View 3D Structure Click here
Q557I4 View 3D Structure Click here
Q55CT4 View 3D Structure Click here
Q55CY7 View 3D Structure Click here
Q59KZ1 View 3D Structure Click here
Q59NB8 View 3D Structure Click here
Q6DGD8 View 3D Structure Click here
Q6K4E7 View 3D Structure Click here
Q6P179 View 3D Structure Click here
Q6Q4G3 View 3D Structure Click here
Q6Z6L4 View 3D Structure Click here
Q7KRW4 View 3D Structure Click here
Q7PLV6 View 3D Structure Click here
Q84TA3 View 3D Structure Click here
Q8BXQ6 View 3D Structure Click here
Q8C129 View 3D Structure Click here
Q8H0S9 View 3D Structure Click here
Q8IEK1 View 3D Structure Click here
Q8IKB4 View 3D Structure Click here
Q8IN25 View 3D Structure Click here
Q8INH6 View 3D Structure Click here
Q8IRH1 View 3D Structure Click here
Q8K093 View 3D Structure Click here
Q8LPF0 View 3D Structure Click here
Q8MRN5 View 3D Structure Click here
Q8N6M6 View 3D Structure Click here
Q8SWX4 View 3D Structure Click here
Q8VCT3 View 3D Structure Click here
Q8VZH2 View 3D Structure Click here
Q95SR0 View 3D Structure Click here
Q9EQH2 View 3D Structure Click here
Q9FY49 View 3D Structure Click here
Q9H4A4 View 3D Structure Click here
Q9HAU8 View 3D Structure Click here
Q9JJ22 View 3D Structure Click here
Q9NZ08 View 3D Structure Click here
Q9TYN3 View 3D Structure Click here
Q9U2H2 View 3D Structure Click here
Q9UIQ6 View 3D Structure Click here
Q9UKU6 View 3D Structure Click here
Q9USX1 View 3D Structure Click here
Q9VAM2 View 3D Structure Click here
Q9VD85 View 3D Structure Click here
Q9VD87 View 3D Structure Click here
Q9VFW9 View 3D Structure Click here
Q9VFX0 View 3D Structure Click here
Q9VJ39 View 3D Structure Click here
Q9VJN2 View 3D Structure Click here
Q9VTL4 View 3D Structure Click here
Q9W1S1 View 3D Structure Click here
Q9W2S7 View 3D Structure Click here
Q9W2S8 View 3D Structure Click here
Q9XVV9 View 3D Structure Click here