jm980351c_si_001.pdf (86.38 kB)
Calculation of the pKa Values for the Ligands and Side Chains of Escherichia coli d-Alanine:d-Alanine Ligase
journal contribution
posted on 1998-12-29, 00:00 authored by Heather A. Carlson, James M. Briggs, J. Andrew McCammonPoisson−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.