title: Crystal structures of penicillin-binding protein 6 from Escherichia coli.
abstract: Penicillin-binding protein 6 (PBP6) is one of the two main DD-carboxypeptidases in Escherichia coli, which are implicated in maturation of bacterial cell wall and formation of cell shape. Here, we report the first X-ray crystal structures of PBP6, capturing its apo state (2.1 A), an acyl-enzyme intermediate with the antibiotic ampicillin (1.8 A), and for the first time for a PBP, a preacylation complex (a "Michaelis complex", determined at 1.8 A) with a peptidoglycan substrate fragment containing the full pentapeptide, NAM-(L-Ala-D-isoGlu-L-Lys-D-Ala-D-Ala). These structures illuminate the molecular interactions essential for ligand recognition and catalysis by DD-carboxypeptidases, and suggest a coupling of conformational flexibility of active site loops to the reaction coordinate. The substrate fragment complex structure, in particular, provides templates for models of cell wall recognition by PBPs, as well as substantiating evidence for the molecular mimicry by beta-lactam antibiotics of the peptidoglycan acyl-D-Ala-D-Ala moiety.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California San Francisco, Byers Hall, Room 508D, 1700 Fourth Street, San Francisco, California 94158-2550, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Chen
authors.forename: Weilie
authors.initials: W
authors.lastname: Zhang
authors.forename: Qicun
authors.initials: Q
authors.lastname: Shi
authors.forename: Dusan
authors.initials: D
authors.lastname: Hesek
authors.forename: Mijoon
authors.initials: M
authors.lastname: Lee
authors.forename: Shahriar
authors.initials: S
authors.lastname: Mobashery
authors.forename: Brian K
authors.initials: BK
authors.lastname: Shoichet
mesh_terms: D000667:Ampicillin / Q000737:chemistry; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004150:Dipeptidases / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D046915:Penicillin-Binding Proteins / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics; D010446:Peptide Fragments / Q000737:chemistry; D013329:Structure-Activity Relationship
chemical_list: D029968:Escherichia coli Proteins; D046915:Penicillin-Binding Proteins; D010446:Peptide Fragments; D000667:Ampicillin; D004150:Dipeptidases; C019989:DD-carboxypeptidase-endopeptidase