title: High resolution structure of an M23 peptidase with a substrate analogue.
abstract: LytM is a Staphylococcus aureus autolysin and a homologue of the S. simulans lysostaphin. Both enzymes are members of M23 metallopeptidase family (MEROPS) comprising primarily bacterial peptidoglycan hydrolases. LytM occurs naturally in a latent form, but can be activated by cleavage of an inhibitory N-terminal proregion. Here, we present a 1.45 Å crystal structure of LytM catalytic domain with a transition state analogue, tetraglycine phosphinate, bound in the active site. In the electron density, the active site of the peptidase, the phosphinate and the "diglycine" fragment on the P1' side of the transition state analogue are very well defined. The density is much poorer or even absent for the P1 side of the ligand. The structure is consistent with the involvement of His260 and/or His291 in the activation of the water nucleophile and suggests a possible catalytic role for Tyr204, which we confirmed by mutagenesis. Possible mechanisms of catalysis and the structural basis of substrate specificity are discussed based on the structure analysis.
authors.affiliation: International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Maja
authors.initials: M
authors.lastname: Grabowska
authors.affiliation: International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Jagielska
authors.affiliation: International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland.|Institute of Biochemistry and Biophysics, Pawinskiego 5a, 02-106 Warsaw, Poland.
authors.forename: Honorata
authors.initials: H
authors.lastname: Czapinska
authors.affiliation: International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland.|Institute of Biochemistry and Biophysics, Pawinskiego 5a, 02-106 Warsaw, Poland.
authors.forename: Matthias
authors.initials: M
authors.lastname: Bochtler
authors.affiliation: International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Izabela
authors.initials: I
authors.lastname: Sabala
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055162:Biocatalysis; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D010450:Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006639:Histidine / Q000737:chemistry; D008024:Ligands; D008248:Lysostaphin / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010721:Phosphinic Acids / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013210:Staphylococcus / Q000737:chemistry* / Q000201:enzymology; D013211:Staphylococcus aureus / Q000737:chemistry* / Q000201:enzymology; D014443:Tyrosine / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D009842:Oligopeptides; D010721:Phosphinic Acids; D014867:Water; D014443:Tyrosine; D006639:Histidine; D010450:Endopeptidases; D008248:Lysostaphin; C120985:LytM protein, Staphylococcus aureus; C046274:glycyl-glycyl-glycyl-glycine