Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase
Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase
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DOI：
10.1021/jm980351c
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发表时间：
1999-01-14
影响因子：
7.3
通讯作者：
McCammon, JA
中科院分区：
文献类型：
--
作者：
Carlson, HA;Briggs, JM;McCammon, JA
泊松-玻尔兹曼静电学方法已用于计算大肠杆菌 (DdlB) ddlb 基因的 D-丙氨酸:D-丙氨酸连接酶的配体和可滴定侧链的 pK(a) 位移。本研究的重点是确定 DdlB 活性位点中第二个 D-丙氨酸 (D-Ala(2)) 的电离状态。胺的 pK(a) 在蛋白质中的碱性增加了 5 pK(a) 单位，这清楚地表明 D-Ala(2) 以两性离子状态与 DdlB 结合，而不是像之前建议的那样以游离碱形式结合。与万古霉素抗性级联的缩酚肽连接酶 VanA 进行了比较。这表明 VanA 由于结合特异性的变化而不是催化行为的改变而具有不同的酶性质，并且 D-乳酸与 D-Ala(2) 的结合特异性可能源于配体电离特性的差异。
Poisson-Boltzmann electrostatics methods have been used to calculate the pK(a) 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-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 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-Ala(2) may arise from the difference in ionization characteristics of the ligands.