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307  structures 18694  species 20  interactions 56090  sequences 118  architectures

Family: Peptidase_M16_C (PF05193)

Summary: Peptidase M16 inactive domain

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Peptidase M16 inactive domain Provide feedback

Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1].

Literature references

  1. Taylor AB, Smith BS, Kitada S, Kojima K, Miyaura H, Otwinowski Z, Ito A, Deisenhofer J; , Structure (Camb) 2001;9:615-625.: Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. PUBMED:11470436 EPMC:11470436

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007863

These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.

The peptidases in this group of sequences include:

  • Insulinase, insulin-degrading enzyme (EC)
  • Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, EC)
  • Pitrlysin, Protease III precursor (EC)
  • Nardilysin, (EC)
  • Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (EC)
  • Coenzyme PQQ synthesis protein F (EC)

These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [PUBMED:7990931] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [PUBMED:11470436].

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 Peptidase_ME (CL0094), which has the following description:

All members of this clan are characterised by a HXXEH motif, which is is involved in zinc binding. Furthermore all members adopt an alpha and beta fold. More specifically, there us a four to six stranded antiparallel beta sheet surrounded by five helices. However, LuxS (PFAM:PF02664) is not a peptidase, although its hydrolytic mechanism of catalysis appears to be conserved [1].

The clan contains the following 4 members:

LuxS Peptidase_M16 Peptidase_M16_C Peptidase_M44


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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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 NCBI

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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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Yeats C
Previous IDs: none
Type: Domain
Author: Yeats C
Number in seed: 139
Number in full: 56090
Average length of the domain: 179.30 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 37.42 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 183
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


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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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There are 20 interactions for this family. More...

Cytochrom_B_N_2 UCR_14kD Ubiq-Cytc-red_N UCR_TM UcrQ Calc_CGRP_IAPP V-set UCR_14kD Hormone_2 UCR_6-4kD M16C_assoc Insulin Beta-APP IL8 Peptidase_M16 M16C_assoc Peptidase_M16_C ANP UCR_6-4kD Peptidase_M16


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_M16_C domain has been found. There are 307 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 seqence.

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