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Studies on the reaction mechanism of peroxidase based on its tertiary structure

基于过氧化物酶三级结构的反应机理研究

基本信息

批准号：
04680055
负责人：
FUKUYAMA Keiichi
金额：
$ 1.09万
依托单位：
Osaka University
依托单位国家：
日本
项目类别：
Grant-in-Aid for General Scientific Research (C)
财政年份：
1992
资助国家：
日本
起止时间：
1992 至 1993
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-04680055/
关键词：
peroxidase X-ray crystallography three-dimensional structure

项目摘要

The reaction mechanism of peroxidase from a fungus Arthromyces ramosus (ARP) has been discussed on the basis of its three-dimensional structure determined by X-ray crystallography.1. The crystal structure of ARP has been determined by the multiple isomorphous replacement method and refined to R=17.4 % for the 19,191 reflections between 7.0 and 1.9 A resolution. The model includes residues 9 to 344, the heme group, two N-acetylglucosamine residues, two calcium ions and 246 water molecules.2. The overall tertiary structure of ARP is similar to that of yeast cytochrome c peroxidase (CCP) and that of the lignin peroxidase from Phanerochaete chrysosporium. Although the histidine and arginine residues (His56 and Arg52) at the distal side of the heme are conserved in the amino acid sequences of various heme peroxidases, the orientations of the side chains of these residues relative to the heme in ARP differ significantly from those in CCP and Lip.In order to explore the role of Arg52 and His56 during the compound I formation, the crystal structure of ARP complexed with a substrate analogue I_3 - has been determined at 2.2 A resolution. Upon I_3" binding the side chain of Arg52 moved little, while that of His56 moved significantly. On the basis of these results the mode of binding of peroxide to the heme has been similated with computer graphics, and the process of the enzyme reaction as well as the role of these residues has been discussed.

根据X射线晶体学测定的多枝节霉菌（Arthromyces ramosus，阿普）过氧化物酶的三维结构，探讨了ARP的反应机理.阿普的晶体结构已通过多重同晶置换法测定，并在7.0和1.9 A分辨率之间的19，191次反射中精确至R= 17.4%。该模型包括第9至344位残基、血红素基团、两个N-乙酰葡糖胺残基、两个钙离子和246个水分子.阿普的总体三级结构类似于酵母细胞色素c过氧化物酶（CCP）和来自黄孢原毛革菌的木质素过氧化物酶。虽然组氨酸和精氨酸残基在各种血红素过氧化物酶的氨基酸序列中，位于血红素远端侧的两个残基（His 56和Arg 52）是保守的，阿普中这些残基相对于血红素的侧链的取向与CCP和Lip中的那些有显著不同。在2.2A分辨率下测定了阿普与底物类似物I_3 -络合物的晶体结构。I_3 ~+结合时，Arg 52侧链移动较小，而His 56侧链移动较大。在此基础上，用计算机图形模拟了过氧化物与血红素的结合方式，并对酶反应的过程和这些残基的作用进行了讨论。