title: Insights into the base catalysis exerted by the DD-transpeptidase from Streptomyces K15: a molecular dynamics study.
abstract: Herein, we present results from molecular dynamics simulations of the DD-transpeptidase/penicillin-binding protein from Streptomyces K15 and its Michaelis complex with benzylpenicillin. For the apo-enzyme, six different configurations of the active site were modeled in aqueous solution and their relative stabilities were estimated by means of quantum mechanical energy calculations. The energetically most stable configuration has a neutral Lys(213) residue. In this configuration, the nucleophilic Ser(35) hydroxyl group interchanges with a water molecule in the "oxy-anion hole" and the Lys(38)/Lys(213) ammonium/amino groups are connected through the Ser(96) hydroxyl group. Subsequently, the enzyme-penicillin complexes corresponding to the four most stable configurations of the apo-enzyme were modeled. In the presence of the beta-lactam antibiotic, the configuration with a neutral Lys(38) residue is favored energetically and shows the best orientation for nucleophilic attack. In addition, a very stable contact between the Ser(35) hydroxyl group and the neutral amino group of Lys(38) supports the assignation of Lys(38) as the base catalyst for the acylation step. Finally, some mechanistic implications of enzyme-inhibitor contacts involving the benzylpenicillin carboxylate group are also discussed.
authors.affiliation: Departamento de Química Física y Analítica, Universidad de Oviedo, C/ Julián Clavería, 8. 33006, Oviedo, Asturias, Spain.
authors.forename: Natalia
authors.initials: N
authors.lastname: Díaz
authors.forename: Tomás L
authors.initials: TL
authors.lastname: Sordo
authors.forename: Dimas
authors.initials: D
authors.lastname: Suárez
mesh_terms: D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D003460:Crystallization; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry; D004795:Enzyme Stability; D008239:Lysine / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D010400:Penicillin G / Q000737:chemistry / Q000378:metabolism; D046915:Penicillin-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D011789:Quantum Theory; D012694:Serine / Q000737:chemistry; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase / Q000737:chemistry* / Q000378:metabolism; D013302:Streptomyces / Q000201:enzymology*; D013816:Thermodynamics
chemical_list: D046915:Penicillin-Binding Proteins; D012694:Serine; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase; D008239:Lysine; D003545:Cysteine; D010400:Penicillin G