title: Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism.
abstract: Escherichia coli signal peptidase (SPase) and E. coli UmuD protease are members of an evolutionary clan of serine proteases that apparently utilize a serine-lysine catalytic dyad mechanism. Recently, the crystallographic structure of a SPase inhibitor complex was solved elucidating the catalytic residues and the substrate binding subsites. Here we show a detailed comparison of the E. coli SPase structure to the native E. coli UmuD' structure. The comparison reveals that despite a very low sequence identity these functionally diverse enzymes share the same protein fold within their catalytic core and allows by analogy for the assignment of the cleavage-site orientation and substrate binding subsites in the UmuD(D') protease. The structural alignment of SPase and UmuD' predicts important mechanistic and structural similarities and differences within these newly characterized families of serine proteases.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Paetzel
authors.forename: N C
authors.initials: NC
authors.lastname: Strynadka
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins; D008239:Lysine; D008565:Membrane Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012694:Serine; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D008565:Membrane Proteins; D012694:Serine; D012697:Serine Endopeptidases; C402410:UmuD protease, E coli; C026515:type I signal peptidase; D008239:Lysine