title: Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.
abstract: The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and maintenance of the cell wall. The model contains a penicillin binding domain similar to known structures, but includes a large insertion which folds into domains with unique folds. The structures of the protein covalently attached to five different antibiotics presented here show the active site residues are unmoved compared to the apoprotein, but nearby surface loops and helices are displaced in some cases. The altered geometry of conserved active site residues compared with those of other PBPs suggests a possible cause for the slow deacylation rate of PBP4.
authors.affiliation: Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kishida
authors.forename: Satoru
authors.initials: S
authors.lastname: Unzai
authors.forename: David I
authors.initials: DI
authors.lastname: Roper
authors.forename: Adrian
authors.initials: A
authors.lastname: Lloyd
authors.forename: Sam-Yong
authors.initials: SY
authors.lastname: Park
authors.forename: Jeremy R H
authors.initials: JR
authors.lastname: Tame
mesh_terms: D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D046915:Penicillin-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; D046915:Penicillin-Binding Proteins; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase; C478706:penicillin-binding protein 4, E coli