Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase
文献类型：期刊论文
| 作者 | Sheng, Xiang1; Gao, Jun1; Liu, Yongjun1,2 ; Liu, Chengbu1
|
| 刊名 | journal of molecular graphics & modelling
 |
| 出版日期 | 2013-07-01 |
| 卷号 | 44页码:17-25 |
| 关键词 | Saccharopine dehydrogenase L-Lysine biosynthesis Density functional theory (DFT) method Proton shuttle Reaction mechanism |
| ISSN号 | 1093-3263 |
| 通讯作者 | liu, yj (reprint author), shandong univ, sch chem & chem engn, key lab theoret & computat chem, jinan 250100, shandong, peoples r china. |
| 中文摘要 | 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. |
| 英文摘要 | 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. |
| WOS标题词 | science & technology ; life sciences & biomedicine ; technology ; physical sciences |
| 类目[WOS] | biochemical research methods ; biochemistry & molecular biology ; computer science, interdisciplinary applications ; crystallography ; mathematical & computational biology |
| 研究领域[WOS] | biochemistry & molecular biology ; computer science ; crystallography ; mathematical & computational biology |
| 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 |
| WOS记录号 | WOS:000324965300003 |
| 公开日期 | 2014-05-09 |
| 源URL | [http://ir.nwipb.ac.cn/handle/363003/3935]  |
| 专题 | 西北高原生物研究所_中国科学院西北高原生物研究所 |
| 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. |
入库方式： OAI收割
来源：西北高原生物研究所
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