Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase

doi:10.1016/j.jmgm.2013.04.009

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	Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase
	Sheng, Xiang 1; Gao, Jun 1; Liu, Yongjun1,2 ; Liu, Chengbu 1
	2013-07-01
发表期刊	JOURNAL OF MOLECULAR GRAPHICS & MODELLING
ISSN	1093-3263
卷号	44 页码:17-25
文章类型	Article
摘要	Saccharopine dehydrogenase (SDH) is the last enzyme in the AAA pathway of L-lysine biosynthesis. On the basis of crystal structures of SDH, the whole catalytic cycle of SDH has been studied by using density functional theory (DFT) method. Calculation results indicate that hydride transfer is the rate-limiting step with an energy barrier of 25.02 kcal/mol, and the overall catalytic reaction is calculated to be endothermic by 9.63 kcal/mol. Residue Lys77 is proved to be functional only in the process of saccharopine deprotonation until the formation of product L-lysine, and residue His96 is confirmed to take part in multiple proton transfer processes and can be described as a proton transfer station. From the point of view of energy, the SDH catalytic reaction for the synthesis of L-lysine is unfavorable compared with its reverse reaction for the synthesis of saccharopine. These results are essentially consistent with the experimental observations from pH dependence of kinetic parameters and isotope effects. (C) 2013 Elsevier Inc. All rights reserved.
关键词	Saccharopine Dehydrogenase L-lysine Biosynthesis Density Functional Theory (Dft) Method Proton Shuttle Reaction Mechanism
WOS标题词	Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences
DOI	10.1016/j.jmgm.2013.04.009
关键词[WOS]	ALPHA-AMINOADIPATE PATHWAY ; DENSITY-FUNCTIONAL THERMOCHEMISTRY ; SACCHAROMYCES-CEREVISIAE ; LYSINE BIOSYNTHESIS ; HOMOCITRATE SYNTHASE ; CATALYTIC MECHANISM ; FUNGI ; EXCHANGE ; METABOLISM ; AUXOTROPHS
收录类别	SCI
语种	英语
项目资助者	National Natural Science Foundation of China(21173129)
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology
WOS记录号	WOS:000324965300003
出版者	ELSEVIER SCIENCE INC
引用统计	被引频次：4[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/3935
专题	中国科学院西北高原生物研究所
通讯作者	Liu, Yongjun
作者单位	1.Shandong Univ, Sch Chem & Chem Engn, Key Lab Theoret & Computat Chem, Jinan 250100, Shandong, Peoples R China 2.Chinese Acad Sci, Northwest Inst Plateau Biol, Xining 810001, Qinghai, Peoples R China
推荐引用方式 GB/T 7714	Sheng, Xiang,Gao, Jun,Liu, Yongjun,et al. Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING,2013,44:17-25.
APA	Sheng, Xiang,Gao, Jun,Liu, Yongjun,&Liu, Chengbu.(2013).Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase.JOURNAL OF MOLECULAR GRAPHICS & MODELLING,44,17-25.
MLA	Sheng, Xiang,et al."Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase".JOURNAL OF MOLECULAR GRAPHICS & MODELLING 44(2013):17-25.

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