Calculation of the pK(a) values for the ligands and side chains of Escherichia coli D-alanine : D-alanine ligase

Citation
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
Citations number
24
Categorie Soggetti
Chemistry & Analysis
Journal title
JOURNAL OF MEDICINAL CHEMISTRY
ISSN journal
00222623 → ACNP
Volume
42
Issue
1
Year of publication
1999
Pages
109 - 117
Database
ISI
SICI code
0022-2623(19990114)42:1<109:COTPVF>2.0.ZU;2-0
Abstract
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.