title: Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase.
abstract: Poisson-Boltzmann electrostatics methods have been used to calculate the pKa shifts for the ligands and titratable side chains of D-alanine:D-alanine ligase of the ddlb gene of Escherichia coli (DdlB). The focus of this study is to determine the ionization state of the second D-alanine (D-Ala2) in the active site of DdlB. The pKa of the amine is shifted over 5 pKa units more alkaline in the protein, clearly implying that D-Ala2 is bound to DdlB in its zwitterionic state and not in the free-base form as had been previously suggested. Comparisons are made to the depsipeptide ligase from the vancomycin-resistance cascade, VanA. It is suggested that VanA has different enzymatic properties due to a change in binding specificity rather than altered catalytic behavior and that the specificity of binding D-lactate over D-Ala2 may arise from the difference in ionization characteristics of the ligands.
authors.affiliation: Departments of Chemistry and Biochemistry and of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, USA.
authors.forename: H A
authors.initials: HA
authors.lastname: Carlson
authors.forename: J M
authors.initials: JM
authors.lastname: Briggs
authors.forename: J A
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D001665:Binding Sites; D004151:Dipeptides / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology*; D008024:Ligands; D010453:Peptide Synthases / Q000378:metabolism*; D017186:Titrimetry
chemical_list: D004151:Dipeptides; D008024:Ligands; C002956:alanylalanine; D010453:Peptide Synthases; C019638:D-alanylalanine synthetase