Family M16


Summary Holotypes Alignment Tree Genomes Structure Literature H-seq M-seq


Summary Holotypes Alignment Tree Genomes Literature


Summary Holotypes Alignment Tree Genomes Literature


Summary Holotypes Alignment Tree Genomes Literature

Summary for family M16

NamePeptidase family M16 (pitrilysin family)
Family type peptidaseM16.001 - pitrilysin (Escherichia coli), MEROPS Accession MER0001222 (peptidase unit: 24-232)
Content of familyPeptidase family M16 contains metalloendopeptidases.
History Identifier created: Biochem.J. 290:205-218 (1993)
Pitrilysin has been reviewed by Roth, 2004, and chapters on seven other peptidases in family M16 are to be found in the same volume.
Catalytic typeMetallo
Active siteTwo of the zinc ligands occur in the motif His-Xaa-Xaa-Glu-His, almost the reverse of the HEXXH motif found in clan MA. The glutamate in this HXXEH motif is important for catalysis, and a glutamate more C-terminal is the third zinc ligand (Becker & Roth, 1992; Taylor et al., 2001). Mutation of glutamate-162 mutant produced a protein that retained 20% of the activity of the wild-type enzyme (Becker & Roth, 1993).
Activities and specificitiesThe specificities of peptidases in family M16 are varied, but the site of cleavage is seldom far from a terminus of the substrate molecule. A possible explanation for this is suggested by the structure of mitochondrial processing peptidase (MPP) (see below) in which the active site is sterically hindered; this may be general in the family. Good assays can be made with oligopeptides that are derivatised as quenched-fluoresence substrates (Anastasi et al., 1993; Song et al., 2001). The specificity of pitrilysin (M16.001) was described by Anastasi et al., 1993. The sites of cleavage by peptidases in the family (see the respective Substrates data pages) often include bonds on the amino side of arginine, and nardilysin (M16.005) has a definite preference for cleavage of XaaArg bonds (Chow et al., 2003). MMP cleaves N-terminal, mitochondrial targeting signals from proteins as they are imported to the mitochondrion. These signal peptides tend to contain basic amino acid residues, and it has been noted that the wall of the active site cavity contains acidic side chains that could explain this specificity (Kitada & Ito, 2001).
Insulysin is activated by thiol compounds (Perlman et al., 1993) which is an unusual characteristic for a metallopeptidase not seen with other members of the family.
InhibitorsLike other metallopeptidases, those in family M16 are inhibited by chelating agents. Some of the peptidases are weakly and non-specifically inhibited by bacitracin, or a bacitracin-zinc complex (e.g. Anastasi et al., 1993). Few potent or specific inhibitors for peptidases in the family have been described.
Molecular structureStructural data are available for MPP, the molecule of which is a heterodimer composed of the catalytically-active beta-subunit (M16.003) and the homologous, but non-peptidase, alpha-subunit (M16.971). The active site of M16.003, structurally similar to that of thermolysin despite the reversal of the motif, is located within a large cavity between the subunits. A glycine-rich region that forms an insert in the alpha-subunit restricts access to the central cavity.
Basis of clan assignmentType family of clan ME.
Distribution of family Bacteria details  
Archaea details  
Protozoa details  
Fungi details  
Plants details  
Animals details  
Viruses details  
Biological functionsMPP removes an N-terminal targeting signal from mitochondrial protein molecules that have been synthesized in the cytoplasm as they are imported into the mitochondrion. There is much interest in the possibility that insulysin (M16.002) may be a physiologically significant alpha-secretase, usefully degrading the amyloidogenic Alzheimer"s beta-peptide (Edland, 2004).
Statistics for family M16Sequences:20037
Identifiers with PDB entries:18
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Subfamily M16A
Name Peptidase subfamily M16A
Subfamily type peptidase M16.001 - pitrilysin (Escherichia coli), MEROPS Accession MER0001222 (peptidase unit: 24-232)
Active site residues H88 E91 H92 E162 E169 
Statistics Sequences: 5944
Identifiers: 23
Identifiers with PDB entries: 5
Other databases HOMSTRAD hs1q2la
PFAM PF00675
PFAM PF05193
SCOP 143501
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
pqqF proteinM16.006-
Axl1 peptidaseM16.007-
Ste23 peptidaseM16.008-
Iph1 peptidase (Schizosaccharomyces pombe) and similarM16.020-
insulysin unit 2M16.982Yes
nardilysin unit 2M16.983-
insulysin unit 3M16.984Yes
nardilysin unit 3M16.987-
At3g57470 (Arabidopsis thaliana)M16.A01-
At2g41790 (Arabidopsis thaliana)-like peptidaseM16.A02-
CG2025 protein (Drosophila melanogaster)M16.A06-
CG10588 protein (Drosophila melanogaster)M16.A07-
C02G6.1 g.p. (Caenorhabditis elegans)M16.A08-
F44E7.4 g.p. (Caenorhabditis elegans)M16.A09-
C28F5.4 g.p. (Caenorhabditis elegans)M16.A10-
C02G6.2 g.p. (Caenorhabditis elegans)M16.A11-
DDB_G0287851 g.p. (Dictyostelium discoideum)M16.A14-
subfamily M16A non-peptidase homologuesnon-peptidase homologueYes
subfamily M16A unassigned peptidasesunassigned-
Subfamily M16B
Name Peptidase subfamily M16B
Subfamily type peptidase M16.003 - mitochondrial processing peptidase beta-subunit (Saccharomyces cerevisiae), MEROPS Accession MER0001229 (peptidase unit: 30-245)
Active site residues H70 E73 H74 E143 E150 
Statistics Sequences: 11777
Identifiers: 22
Identifiers with PDB entries: 12
Other databases CATH 3.30.830.10
HOMSTRAD Peptidase_M16
PFAM PF00675
PFAM PF05193
SCOP 63412
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
mitochondrial processing peptidase beta-subunitM16.003Yes
chloroplast (stromal) processing peptidaseM16.004-
hydrogenosomal processing peptidaseM16.015-
YMXG peptidaseM16.016-
YMXG peptidaseM16.019Yes
SPH2682 protein (Sphingomonas sp. strain A1)M16.970Yes
mitochondrial processing peptidase non-peptidase alpha subunitM16.971Yes
ubiquinol-cytochrome c reductase core protein IM16.973Yes
ubiquinol-cytochrome c reductase core protein IIM16.974Yes
Mername-AA224 non-peptidase homologueM16.975-
mitochondrial processing peptidase beta-like proteinM16.977-
protein similar to mitochondrial processing peptidase beta (Rattus norvegicus)M16.978-
mitochondrial processing peptidase beta subunit domain 2M16.980-
ubiquinol-cytochrome c reductase core protein domain 2M16.981Yes
mitochondrial processing peptidase subunit alpha unit 2M16.985Yes
Fjoh_2253 protein (Flavobacterium johnsoniae)M16.986Yes
At5g56730 (Arabidopsis thaliana)-like peptidaseM16.A03-
PqqL protein (Escherichi coli)M16.A05-
BSSC8_26020 g.p. (Bacillus subtilis)M16.A15Yes
albF g.p. (Bacillus subtilis)M16.A16-
ymfH g.p. (Bacillus subtilis)M16.A20-
PF14_0382 g.p. (Plasmodium falciparum)M16.A21-
LOC133083 g.p. (Homo sapiens)M16.P01-
subfamily M16B non-peptidase homologuesnon-peptidase homologueYes
subfamily M16B unassigned peptidasesunassignedYes
Subfamily M16C
Name Peptidase subfamily M16C
Subfamily type peptidase M16.009 - eupitrilysin (Homo sapiens), MEROPS Accession MER0004877 (peptidase unit: 96-243)
Active site residues H104 E107 H108 E180 E205 
Statistics Sequences: 2338
Identifiers: 11
Identifiers with PDB entries: 1
Other databases INTERPRO IPR011249
PFAM PF00675
PFAM PF05193
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
PreP1 peptidase (Arabidopsis-type)M16.012Yes
CYM1 peptidase (Saccharomyces cerevisiae)M16.013-
PreP2 peptidase (Arabidopsis-type)M16.018-
insulysin homologue (Saccharomyces cerevisiae)M16.A04-
C05D11.1 g.p. (Caenorhabditis elegans)M16.A12-
DDB_G0287909 g.p. (Dictyostelium discoideum)M16.A17-
DDB_G0290415 g.p. (Dictyostelium discoideum)M16.A18-
cym1 g.p. (Schizosaccharomyces pombe)M16.A19-
PF11_0189 g.p. (Plasmodium falciparum)M16.A22-
subfamily M16C non-peptidase homologuesnon-peptidase homologue-
subfamily M16C unassigned peptidasesunassigned-
Peptidases not assigned to subfamily
Peptidases and Homologues MEROPS ID Structure
Y70C5C.1 g.p. (Caenorhabditis elegans)M16.A13-
family M16 non-peptidase homologuesnon-peptidase homologue-
family M16 unassigned peptidasesunassigned-