Puig Eduard, Garcia-Viloca Mireia, Gonzalez-Lafont Angels, Lluch José M, Field Martin J
Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
J Phys Chem B. 2007 Mar 8;111(9):2385-97. doi: 10.1021/jp066350a. Epub 2007 Feb 8.
The mechanism of the reactions catalyzed by the pyridoxal-phosphate-independent amino acid racemases and epimerases faces the difficult task of deprotonating a relatively low acidicity proton, the amino acid's alpha-hydrogen, with a relatively poor base, a cysteine. In this work, we propose a mechanism for one of these enzymes, glutamate racemase (MurI), about which many controversies exist, and the roles that its active site residues may play. The titration curves and the pK1/2 values of all of the ionizable residues for different structures leading from reactants to products have been analyzed. From these results a concerted mechanism has been proposed in which the Cys70 residue would deprotonate the alpha-hydrogen of the substrate while, at the same time, being deprotonated by the Asp7 residue. To study the consistency of this mechanism classical molecular dynamics (MD) simulations have been carried out along with pK1/2 calculations on the MD-generated structures.
磷酸吡哆醛非依赖性氨基酸消旋酶和差向异构酶所催化反应的机制面临着一项艰巨任务，即要用一个碱性相对较弱的半胱氨酸去使一个酸性相对较低的质子（氨基酸的α-氢）去质子化。在这项工作中，我们提出了这些酶之一——谷氨酸消旋酶（MurI）的一种机制，关于该机制存在许多争议，同时还提出了其活性位点残基可能发挥的作用。我们分析了从反应物到产物的不同结构中所有可电离残基的滴定曲线和pK1/2值。基于这些结果，我们提出了一种协同机制，其中半胱氨酸70残基会使底物的α-氢去质子化，与此同时，它自身又会被天冬氨酸7残基去质子化。为了研究该机制的一致性，我们进行了经典分子动力学（MD）模拟，并对MD生成的结构进行了pK1/2计算。
