Family C56


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

Summary for family C56

NamePeptidase family C56 (PfpI endopeptidase family)
Family type peptidaseC56.001 - PfpI peptidase (Pyrococcus furiosus), MEROPS Accession MER0002455 (peptidase unit: 27-162)
Content of familyPeptidase family C56 contains the putative PfpI endopeptidase of Pyrococcus furiosus.
History Identifier created: MEROPS 5.4 (23 March 2001)
The discovery and characterisation of the PfpI endopeptidase (C56.001) have been reviewed by Hicks et al., 2004.
Catalytic typeCysteine
Active site residuesE74 C100 H101 
Active siteActive site residues are proposed to be Cys100 and His101 in Pyrococcus furiosus PfpI endopeptidase (see the Alignment) (Du et al., 2000). It is evidently not possible for the side chains of these adjacent residues to interact to form a catalytic dyad in one polypeptide chain, but in the crystal, the enzyme forms a hexameric ring structure, and the active sites are proposed to be formed at the interfaces between three pairs of monomers. Functional catalytic dyads formed by residues from different subunits are not known from any other family of peptidases. Putative catalytic triads have been recognised in crystal structures: Cys/His/Glu in the yeast YDR533c protein (C56.004) (Graille et al., 2004) and Cys/His/Asp in Escherichia coli Hsp31 (C56.006) (Zhao et al., 2003). These have the geometry expected of catalytic triads similar to that of papain.
Activities and specificitiesThe only member of the family for which peptidase activity has been reported is the PfpI endopeptidase (C56.001). This shows a preference for bulky, hydrophobic P1 residues, and Suc-Ala-Ala-Phe-NHMec serves is a test substrate (Halio et al., 1997). The enzyme acts only on peptides of less than 20 amino acids (Hicks et al., 2004). It should be noted that the specificity for hydrophobic P1 residues is similar to that of peptidases in family S8, which are also expressed by Pyrococcus furiosus, so care is needed in distinguishing the two activities.
InhibitorsAn early study indicated that PfpI endopeptidase is inhibited by PMSF and DFP, and not by iodoacetate (Blumentals et al., 1990; Hicks et al., 2004). This was indicative of a serine peptidase rather than a cysteine peptidase, and further work is needed.
Molecular structureThe structure of PfpI endopeptidase (C56.001) was reported by Du et al. (2000), and structures are also available for the homologues yeast YDR533c protein (C56.004) (Graille et al., 2004) and Escherichia coli Hsp31 (C56.006) (Zhao et al., 2003). The proteins have the alpha/beta hydrolase fold, and are placed in subclan PC(C) because of their structural resemble to aspartyl dipeptidase (S51.001), the type peptidase of clan PC.
Basis of clan assignmentProtein fold of the peptidase unit for members of this family resembles aspartyl dipeptidase, the type example for clan PC.
Distribution of family Bacteria details  
Archaea details  
Protozoa details  
Fungi -  
Plants details  
Animals details  
Viruses -  
Biological functions
Statistics for family C56Sequences:13623
Identifiers with PDB entries:10
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Other databases CATH
PFAM PF01965
PFAM PF13278
PFAM PF13507
SCOP 52325
Peptidases and Homologues MEROPS ID Structure
PfpI peptidaseC56.001Yes
DJ-1 putative peptidaseC56.002Yes
Mername-AA100 putative peptidaseC56.003-
YDR533C putative peptidaseC56.004Yes
Hsp31 peptidaseC56.006Yes
Mername-AA101 non-peptidase homologueC56.971-
phosphoribosylformylglycinamidine synthaseC56.972-
Mername-AA234 non-peptidase homologueC56.973-
Mername-AA296 non-peptidase homologueC56.974-
ES1 protein homolog, mitochondrialC56.975Yes
protein deglycase 2C56.976Yes
At3g02720 (Arabidopsis thaliana)C56.A01Yes
At3g54600 (Arabidopsis thaliana)C56.A02-
chromosome XV reading frame ORF yor391c (Saccharomyces cerevisiae)C56.A03Yes
protein SNO4 (Saccharomyces cerevisiae)C56.A04Yes
SPCC757.03c (Schizosaccharomyces pombe)C56.A05-
DDB_G0276405 (Dictyostelium discoideum)C56.A06-
Family C56 non-peptidase homologuesnon-peptidase homologueYes
Family C56 unassigned peptidasesunassigned-