Family A31


Summary Holotypes Alignment Tree Genomes Structure Literature

Summary for family A31

NamePeptidase family A31 (HybD endopeptidase family)
Family type peptidaseA31.001 - HybD peptidase (Escherichia coli), MEROPS Accession MER0002089 (peptidase unit: 1-161)
Content of familyPeptidase family A31 contains endopeptidases.
History Identifier created: MEROPS 7.3 (22 December 2005)
[NiFe]Hydrogenases are synthesized as two subunits 30-35 kDa and 60-65 kDa in size. The large subunit contains the metallo centre, and once nickel has been bound in this, the subunit is processed to the active enzyme by cleavage at a conserved site near the C-terminus. The hydrogenase maturation endopeptidases of family A31 are responsible for these cleavages.
Catalytic typeAspartic
Active site residuesD,E16 D62 H93 
Active siteEvidence about the active site and catalytic mechanism is indirect. Three residues are strictly conserved: Asp/Glu16, Asp62 and His93 (see the Alignment). These are the residues that are seen to bind cadmium in the crystal structure, and are proposed to bind nickel in the enzyme-substrate complex. The mutations D16N, D62N and D62M of HycI endopeptidase (A31.003) eliminated activity, whereas H93Q displayed a low level of activity (Theodoratou et al., 2000). Since the binding of nickel is in any case required for activity, it cannot safely be concluded that the essential acidic residues have catalytic functions in their own right, but the possibility is strengthened by similarities in location and surrounding motifs of these residues to those that are implicated in the activity of the homologous gpr peptidase (A25.001).
Activities and specificitiesHycI endopeptidase releases a 32-residue C-terminal peptide by cleavage of an -ArgMet- bond closely following the nickel binding site in hydrogenase 3. The specificity for amino acids in the P1 and P1" positions has been investigated by mutagenesis (Theodoratou et al., 2000). HybD endopeptidase (A31.001) cleaves following the equivalent -HisMet- bond in hydrogenase 2, removing 15 residues (Menon et al., 1993). Processing of either hydrogenase can take place only after the nickel atom has been incorporated into the large subunit (Theodoratou et al., 2000).
InhibitorsPeptidase activity is not inhibited by PMSF, benzamidine or EDTA (Rossmann et al., 1995).
Molecular structureBoth HycI and HybD are small, monomeric proteins. The tertiary structure of HybD shows a twisted beta sheet surrounded by three alpha helices on one side and four on the other (Fritsche et al., 1999). A cadmium ion from the crystallization buffer is bound to the molecule, penta-coordinated by Glu16 (two ligands), Asp62, His93, and a water molecule in a pseudo-tetragonal arrangement. It is proposed that the cobalt site binds nickel under more natural circumstances, and is responsible for the absolute requirement of the peptidase for a substrate molecule with bound nickel (Fritsche et al., 1999). The fold of HybD peptidase is similar to that of gpr peptidase (A25.001), and accordingly families A31 and A25 are placed together in clan AE.
Basis of clan assignmentType family of clan AG.
Distribution of family Bacteria details  
Archaea details  
Protozoa -  
Fungi -  
Plants details  
Animals details  
Viruses -  
Biological functionsThe functions of HycI and HybD are in the processing of the precursors of bacterial hydrogenases to their active forms. It is believed that the precursor has an open conformation facilitating coordination of the metal ligand, and that once the metal ion is in place, cleavage of the precursor causes a conformational change that locks the metal in place.
ReviewsTheodoratou et al. (2005)
Statistics for family A31Sequences:2039
Identifiers with PDB entries:1
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
HybD peptidaseA31.001Yes
HyaD peptidaseA31.002-
HycI peptidaseA31.003-
hoxW peptidaseA31.004-
hupW peptidaseA31.005-
FrxA peptidaseA31.006-
TK2004 peptidaseA31.007-
TK2066 peptidaseA31.008-
family A31 non-peptidase homologuesnon-peptidase homologue-
family A31 unassigned peptidasesunassigned-