Ha. Carlson et al., Calculation of the pK(a) values for the ligands and side chains of Escherichia coli D-alanine : D-alanine ligase, J MED CHEM, 42(1), 1999, pp. 109-117
Poisson-Boltzmann electrostatics methods have been used to calculate the pK
(a) shifts for the ligands and titratable side chains of D-alanine:D-alanin
e ligase of the ddlb gene of Escherichia coli (DdlB). The focus of this stu
dy is to determine the ionization state of the second D-alanine (D-Ala(2))
in the active site of DdlB. The pK(a) of the amine is shifted over 5 pK(a)
units more alkaline in the protein, clearly implying that D-Ala(2) is bound
to DdlB in its zwitterionic state and not in the free-base form as had bee
n previously suggested. Comparisons are made to the depsipeptide ligase fro
m the vancomycin-resistance cascade, VanA. It is suggested that VanA has di
fferent enzymatic properties due to a change in binding specificity rather
than altered catalytic behavior and that the specificity of binding D-lacta
te over D-Ala(2) may arise from the difference in ionization characteristic
s of the ligands.