Family C54


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

Summary for family C54

NamePeptidase family C54 (Aut2 peptidase family)
Family type peptidaseC54.003 - autophagin-1 (Homo sapiens), MEROPS Accession MER0013561 (peptidase unit: 28-342)
Content of familyFamily C54 contains endopeptidases with specificity for glycyl bonds.
History Identifier created: MEROPS 5.3 (4 December 2000)
It was discovered by Kirisako et al. (2000) that yeast Apg4/Aut2, now termed Atg4 (C54.001), as an essential component of the cytoplasm-to-vacuole targeting (Cvt) pathway. In eukaryotic cells generally, the membrane fusion events that are made possible by the autophagins lead to autophagy, a major system for the bulk degradation of intracellular proteins. In autophagy, cellular components become enclosed in double membranes to form autophagosomes, and the sequestered proteins are then degraded by the action of lysosomal peptidases. Mammalian peptidases in family C54 are also implicated in the processing and deconjugation of proteins in a number of cell-signalling pathways.
Catalytic typeCysteine
Active site residuesY54 C74 D278 H280 
Active siteThe active site cysteine in autophagin-1 (C54.003) has been identified by site-directed mutagenesis (Tanida et al., 2004). From the crystal structure, a Cys, Asp, His catalytic triad has been identified. Although the fold is similar to that of papain (C01.001), the active site residues are in a different order and the residue that corresponds to the glutamine in papain that helps stabilize the oxyanion hole is a tyrosine in autophagin-1 (Sugawara et al., 2005).
Activities and specificitiesATG4 peptidase (C54.001) makes a single cleavage (Gly116Arg) to release the C-terminal Arg of the protein Apg8/Aut7. However, the enzyme is an endopeptidase and not a carboxypeptidase because it cleaves the same bond even if a peptide replaces the C-terminal Arg; Gly116 is essential, however. Exposure of the new C-terminal Gly of the substrate permits the attachment of a phosphatidylethanolamine moiety, enabling the protein to be attached to membrane lipids, which is essential in the Cvt pathway. ATG4 also releases phosphatidylethanolamine from the Apg8 conjugate in a second reaction in the same pathway, again cleaving a GlyXaa bond. This second reaction is analogous to that performed by deubiquitinating enzymes (e.g. families C12, C19) which recycle ubiquitin from its conjugates. ATG4 can also cleave artificial substrates such as Boc-Thr-Phe-GlyNHMec (Kirisako & Ohsumi, 2004). The mammalian autophagin-3 (C48.003) has been shown to cleave proteins involved in intra-Golgi transport (GATE-16) and receptor sorting (GARARAP) as well as autophagy (MAP1-LC3) (Hemelaar et al., 2003, Tanida et al., 2004). Human autophagin-2 (C54.002) has been shown to cleave GATE-16 at the penultimate GlyPhe bond (Scherz-Shouval et al., 2003).
InhibitorsATG4 peptidase is inhibited by N-ethylmaleimide, but not by E64d (Kirisako & Ohsumi, 2004).
Molecular structureThe crystal structure of human autophagin-1 (Kumanomidou et al., 2005; Sugawara et al., 2005) shows that the fold consists of two domains. The domain that carries the active site residues has a fold similar to that of papain, hence family C54 in included in clan CA. The small, second domain has an alpha/beta fold, and is probably required for interaction with substrates .
Distribution of family Bacteria details  
Archaea -  
Protozoa details  
Fungi details  
Plants details  
Animals details  
Viruses -  
Biological functionsFamily C54 endopeptidases activate and delipidate proteins important in a number of intracellular signalling pathways that involve transfer of proteins across membranes, including autophagy, intra-Golgi transport and receptor sorting.
ReviewsKirisako & Ohsumi (2004)
Statistics for family C54Sequences:1811
Identifiers with PDB entries:2
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
ATG4 peptidaseC54.001-
ATG4.2 peptidase (Leishmania-type)C54.007-
atg-4.1 peptidase (Caenorhabditis elegans-type)C54.008-
atg-4.2 peptidase (Caenorhabditis elegans-type)C54.009-
autophagin-2 (Trypanosoma cruzi)C54.010-
At2g44140 (Arabidopsis thaliana)C54.011-
At3g59950 (Arabidopsis thaliana)C54.012-
Mername-AA151 peptidaseC54.951-
CG6194 protein (Drosophila melanogaster)C54.A03-
CG4428 protein (Drosophila melanogaster)C54.A04-
atg4 peptidase (Schizosaccharomyces pombe-type)C54.A07-
atg4-2 peptidase (Dictyostelium discoideum)C54.A08-
DDB_G0283753 (Dictyostelium discoideum)C54.A09-
Mername-AA192 inactive peptidase homologueC54.P01-
family C54 non-peptidase homologuesnon-peptidase homologue-
family C54 unassigned peptidasesunassigned-