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:
- 金额:$ 1.09万
- 依托单位:
- 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:
- 关键词:
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.
利用x射线晶体学对真菌长节真菌(Arthromyces ramosus, ARP)过氧化物酶的三维结构进行了分析,探讨了过氧化物酶的反应机理。用多重同构置换法确定了ARP的晶体结构,并对7.0 ~ 1.9 A分辨率的19191次反射进行了R= 17.4%的细化。该模型包括9 ~ 344残基、血红素基、两个n -乙酰氨基葡萄糖残基、两个钙离子和246个水分子。ARP的三级结构与酵母细胞色素c过氧化物酶(CCP)和黄孢原毛毛菌的木质素过氧化物酶相似。尽管在各种血红素过氧化物酶的氨基酸序列中,位于血红素远端的组氨酸和精氨酸残基(His56和Arg52)是保守的,但ARP中这些残基相对于血红素的侧链取向与CCP和Lip有显著不同。为了探索Arg52和His56在化合物I形成过程中的作用,在2.2 a分辨率下测定了ARP与底物类似物I_3 -络合的晶体结构。当I_3结合时,Arg52的侧链移动不大,而His56的侧链移动明显。在这些结果的基础上,用计算机图形模拟了过氧化物与血红素的结合方式,并讨论了酶反应的过程以及这些残基的作用。
项目成果
期刊论文数量(16)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
N.Kunishima, K.Fukuyama, S.Wakabayashi, M.Sumida, M.Takaya, Y.Shibano, T.Amachi, and H.Matsubara: "Crystallization and Preliminary X-Ray Differation Studies of Peroxidase From a Fungus Arthromyces ramosus" PROTEINS : Struct. Func. Genet.15. 216-220 (1993)
N.Kunishima、K.Fukuyama、S.Wakabayashi、M.Sumida、M.Takaya、Y.Shibano、T.Amachi 和 H.Matsubara:“来自真菌节节霉菌的过氧化物酶的结晶和初步 X 射线衍射研究”
- DOI:
- 发表时间:
- 期刊:
- 影响因子:0
- 作者:
- 通讯作者:
N.Kunishima, K.Fukuyama, T.Kubota, H.Matsubara, and I.Morishima: "Crystal Structure of Arthromyces ramosus Peroxidase Complexed with Triiodide : Behavior of Arg52 and His56 During the Compound I Formation" (in preparation).
N.Kunishima、K.Fukuyama、T.Kubota、H.Matsubara 和 I.Morishima:“Arthromyces ramosus 过氧化物酶与三碘化物复合的晶体结构:在化合物 I 形成过程中 Arg52 和 His56 的行为”(准备中)。
- DOI:
- 发表时间:
- 期刊:
- 影响因子:0
- 作者:
- 通讯作者:
Naoki Kunishima: "Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase From a Fungus Arthromyces ramosus" PROTEINS:Structure,Function,and Genetics. 15. 216-220 (1993)
Naoki Kunishima:“来自真菌节节霉菌的过氧化物酶的结晶和初步 X 射线衍射研究”蛋白质:结构、功能和遗传学。
- DOI:
- 发表时间:
- 期刊:
- 影响因子:0
- 作者:
- 通讯作者:
N.Kunishima, K.Fukuyama, H.Matsubara, H.Hatanaka, Y.Shibano, and T.Amachi: "Crystal structure of the Fungal peroxidase from Arthromyces ramosus at 1.9 A Resolution : Structural Comparisons with the Lignin and Cytochrome c Peroxidases" J.Mol. Biol.235. 331
N.Kunishima、K.Fukuyama、H.Matsubara、H.Hatanaka、Y.Shibano 和 T.Amachi:“1.9 A 分辨率下节枝菌真菌过氧化物酶的晶体结构:与木质素和细胞色素 c 过氧化物酶的结构比较”
- DOI:
- 发表时间:
- 期刊:
- 影响因子:0
- 作者:
- 通讯作者:
Naoki Kunishima: "Crystal Structure of the Fungal Peroxidase from Arthromyces ramosus at 1.9 〓 Resolution" Journal of Molecular Biology. 235. 331-344 (1994)
Naoki Kunishima:“1.9 〓 分辨率下来自节枝菌的真菌过氧化物酶的晶体结构”《分子生物学杂志》235. 331-344 (1994)。
- DOI:
- 发表时间:
- 期刊:
- 影响因子:0
- 作者:
- 通讯作者:
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
FUKUYAMA Keiichi其他文献
FUKUYAMA Keiichi的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('FUKUYAMA Keiichi', 18)}}的其他基金
Elucidation of mechanisms of bilin synthesizing enzyme and photo-adaptation regulating protein
胆素合成酶和光适应调节蛋白机制的阐明
- 批准号:
23370052 - 财政年份:2011
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for Scientific Research (B)
Elucidation of molecular mechanism of bilin synthesis by ferredoxin-dependent bilin reductases
阐明铁氧还蛋白依赖性胆素还原酶合成胆素的分子机制
- 批准号:
20370037 - 财政年份:2008
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for Scientific Research (B)
Elucidation of reaction mechanism ofthe enzymes involved in the syntbssis of photosynthetic pigments
光合色素合成酶反应机制的阐明
- 批准号:
18570105 - 财政年份:2006
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Functional analysis of proteins based on the tertiary structures focussing on hydrogen atom positions
基于以氢原子位置为重点的三级结构的蛋白质功能分析
- 批准号:
14580674 - 财政年份:2002
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Mechanism of DNA excision repair based on the three-dimensional structure of UvrABC endonuclease
基于UvrABC核酸内切酶三维结构的DNA切除修复机制
- 批准号:
12680659 - 财政年份:2000
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Analysis of assembly mechanism of spherical virus based on its high resolution three-dimensional structure
基于高分辨率三维结构的球形病毒组装机制分析
- 批准号:
10680634 - 财政年份:1998
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Crystallographic and Genetic Study of Cytochrome bc1 Complex
细胞色素bc1复合物的晶体学和遗传学研究
- 批准号:
08044203 - 财政年份:1996
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for international Scientific Research
Study 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
- 批准号:
06680654 - 财政年份:1994
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for General Scientific Research (C)
X-Ray Crystallographic Analysis of Spherical Plant Viruses
球形植物病毒的 X 射线晶体学分析
- 批准号:
61580049 - 财政年份:1986
- 资助金额:
$ 1.09万 - 项目类别:
Grant-in-Aid for General Scientific Research (C)
相似海外基金
CHEMICAL SCREENING AND OPTIMIZATION FACILITY - PROTEIN EXPRESSION AND/OR X-RAY CRYSTALLOGRAPHY
化学筛选和优化设施 - 蛋白质表达和/或 X 射线晶体学
- 批准号:
10942884 - 财政年份:2023
- 资助金额:
$ 1.09万 - 项目类别:
Taking Snapshots of Enzymatic Reactions Using X-ray Crystallography and Spectroscopy
使用 X 射线晶体学和光谱学拍摄酶反应快照
- 批准号:
10623717 - 财政年份:2023
- 资助金额:
$ 1.09万 - 项目类别:
EAGER: JOINT CRYO NEUTRON/X-RAY CRYSTALLOGRAPHY OF RNA AND RNA-PROTEIN INTERACTIONS
EAGER:RNA 和 RNA-蛋白质相互作用的联合冷冻中子/X 射线晶体学
- 批准号:
2224897 - 财政年份:2022
- 资助金额:
$ 1.09万 - 项目类别:
Standard Grant
Protein structure-based enhancement of enzyme performance for food and bioproduct applications using X-ray crystallography, protein modification and metabolic engineering methods
使用 X 射线晶体学、蛋白质修饰和代谢工程方法,基于蛋白质结构增强食品和生物产品应用中的酶性能
- 批准号:
RGPIN-2016-06209 - 财政年份:2021
- 资助金额:
$ 1.09万 - 项目类别:
Discovery Grants Program - Individual
Time-Resolved X-ray Crystallography of Dynamics in Cysteine-Dependent Enzymes
半胱氨酸依赖性酶动力学的时间分辨 X 射线晶体学
- 批准号:
10684770 - 财政年份:2020
- 资助金额:
$ 1.09万 - 项目类别:
Time-Resolved X-ray Crystallography of Dynamics in Cysteine-Dependent Enzymes
半胱氨酸依赖性酶动力学的时间分辨 X 射线晶体学
- 批准号:
10259757 - 财政年份:2020
- 资助金额:
$ 1.09万 - 项目类别:
Elucidating the Hidden Steps of Replicative DNA Synthesis by Time-Resolved X-ray Crystallography
通过时间分辨 X 射线晶体学阐明复制 DNA 合成的隐藏步骤
- 批准号:
2001434 - 财政年份:2020
- 资助金额:
$ 1.09万 - 项目类别:
Standard Grant
Time-Resolved X-ray Crystallography of Dynamics in Cysteine-Dependent Enzymes
半胱氨酸依赖性酶动力学的时间分辨 X 射线晶体学
- 批准号:
10099548 - 财政年份:2020
- 资助金额:
$ 1.09万 - 项目类别:
Optimizing protein expression for X-ray crystallography studies and medicinal chemistry
优化 X 射线晶体学研究和药物化学的蛋白质表达
- 批准号:
552236-2020 - 财政年份:2020
- 资助金额:
$ 1.09万 - 项目类别:
University Undergraduate Student Research Awards
Protein structure-based enhancement of enzyme performance for food and bioproduct applications using X-ray crystallography, protein modification and metabolic engineering methods
使用 X 射线晶体学、蛋白质修饰和代谢工程方法,基于蛋白质结构增强食品和生物产品应用中的酶性能
- 批准号:
RGPIN-2016-06209 - 财政年份:2020
- 资助金额:
$ 1.09万 - 项目类别:
Discovery Grants Program - Individual