Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.
Structure:1CFZ_A; E. coli Hydrogenase Maturating Endopeptidase HybD bound to Cd; contact residues defined by 3.5 A.
Comment:Cd-binding site in this structure is predicted to be the same as the actual Ni-binding site
Comment:Replacement of the homologous metal binding residues in HycI (hydrogenase 3 processing endopeptidase) by site-directed mutagenesis suggest a role in catalysis.
Jiyao W et al.(2023). "The conserved domain database in 2023.",