QM/MM study of the conversion mechanism of lysine to methylornithine catalyzed by methylornithine synthase (PylB)
文献类型:期刊论文
作者 | Zhu, Wenyou ; Liu, Yongjun ; Zhang, Rui ; Liu, YJ (reprint author), Shandong Univ, Sch Chem & Chem Engn, Key Lab Colloid & Interface Chem, Minist Educ, Jinan 250100, Shandong, Peoples R China. |
刊名 | THEORETICAL CHEMISTRY ACCOUNTS
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出版日期 | 2013-09-01 |
英文摘要 | Methylornithine synthase (PylB) belongs to the family of radical SAM enzymes which converts (2S)-lysine to (2R,3R)-3-methylornithine in a radical mechanism. In this paper, the mechanism of lysine mutase reaction catalyzed by PylB has been studied by using quantum mechanics/molecular mechanics approach. The calculations reveal that the PylB-catalyzed reaction follows a fragmentation-recombination mechanism involving seven elementary reaction steps. Both the hemolytic cleavage of C alpha-C beta bond of lysine and the ligation of glycyl radical with aminobutene are possible rate limiting, corresponding to the calculated energy barriers of 23.0 and 24.1 kcal/mol, respectively. The intramolecular rotation of a fragment (aminobutene) can well explain the stereochemistry of the final product. Asp 279 functions as a general acid/base, and the other pocket residues such as Asp112, Arg235, and Ser277 form a network of hydrogen bonds responsible for orientation of the substrate.; Methylornithine synthase (PylB) belongs to the family of radical SAM enzymes which converts (2S)-lysine to (2R,3R)-3-methylornithine in a radical mechanism. In this paper, the mechanism of lysine mutase reaction catalyzed by PylB has been studied by using quantum mechanics/molecular mechanics approach. The calculations reveal that the PylB-catalyzed reaction follows a fragmentation-recombination mechanism involving seven elementary reaction steps. Both the hemolytic cleavage of C alpha-C beta bond of lysine and the ligation of glycyl radical with aminobutene are possible rate limiting, corresponding to the calculated energy barriers of 23.0 and 24.1 kcal/mol, respectively. The intramolecular rotation of a fragment (aminobutene) can well explain the stereochemistry of the final product. Asp 279 functions as a general acid/base, and the other pocket residues such as Asp112, Arg235, and Ser277 form a network of hydrogen bonds responsible for orientation of the substrate. |
源URL | [http://210.75.249.4/handle/363003/3930] ![]() |
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 |
推荐引用方式 GB/T 7714 | Zhu, Wenyou,Liu, Yongjun,Zhang, Rui,et al. QM/MM study of the conversion mechanism of lysine to methylornithine catalyzed by methylornithine synthase (PylB)[J]. THEORETICAL CHEMISTRY ACCOUNTS, Zhu, WY; Liu, YJ; Zhang, R.QM/MM study of the conversion mechanism of lysine to methylornithine catalyzed by methylornithine synthase (PylB),THEORETICAL CHEMISTRY ACCOUNTS,2013,132(9):,2013. |
APA | Zhu, Wenyou,Liu, Yongjun,Zhang, Rui,&Liu, YJ .(2013).QM/MM study of the conversion mechanism of lysine to methylornithine catalyzed by methylornithine synthase (PylB).THEORETICAL CHEMISTRY ACCOUNTS. |
MLA | Zhu, Wenyou,et al."QM/MM study of the conversion mechanism of lysine to methylornithine catalyzed by methylornithine synthase (PylB)".THEORETICAL CHEMISTRY ACCOUNTS (2013). |
入库方式: OAI收割
来源:西北高原生物研究所
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