PMID:9888837

Citation	Carlson, HA, Briggs, JM and McCammon, JA (1999) Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase. J. Med. Chem. 42:109-17
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.
Links	PubMed Online version:10.1021/jm980351c
Keywords	Binding Sites; Dipeptides/metabolism; Escherichia coli/enzymology; Ligands; Peptide Synthases/metabolism; Titrimetry
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