Theoretical Study of the Mechanism of Proton Transfer in the Esterase Estb from Burkholderia Gladioli

doi:10.1021/jp206297d

CORC > 上海药物研究所 > 中国科学院上海药物研究所 > 药物发现与设计中心

	Theoretical Study of the Mechanism of Proton Transfer in the Esterase Estb from Burkholderia Gladioli
	Chen, Liang 1,2; Kong, Xiangqian 2; Liang, Zhongjie 2; Ye, Fei 2; Yu, Kunqian2 ; Dai, Weiyi 1; Wu, Daocheng 1; Luo, Cheng2,3 ; Jiang, Hualiang2
刊名	JOURNAL OF PHYSICAL CHEMISTRY B
	2011-11-10
卷号	115 期号:44 页码:13019-13025
ISSN号	1520-6106
DOI	10.1021/jp206297d
文献子类	Article
英文摘要	Esterase EstB from Burkholderia gladioli belongs to a novel class of esterases homologous to penicillin binding proteins, notably DD-peptidase and class C beta-lactamases. It can cleave the side chain acetyl ester group from cephalosporins leaving the beta-lactam ring intact, which is a feature of relevance to industrial biocatalytic applications in the production of semisynthetic cephalosporin derivatives. Due to its important role as a potential biocatalyst in industry, the significance of EstB has been greatly appreciated. However, the molecular basis for those residues involving catalysis of EstB remains elusive. By analyzing the crystal structure of EstB, we identified a conserved water molecule in active-site cavity which might mediate an intramolecular proton transfer (PT) from Lys78 to Asp186 via Tyr133. Then a combined computational approach including molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations was employed to explore this presumable PT mode in the native enzyme. A 30 ns MD simulation of the enzyme highlights the conserved H-bond network involving Lys78, Tyr133, Asp186, and the conserved water molecule in the active site. In particular, the water molecule did not exchange with bulk solvent, indicating its structural and functional relevance. The energy profile calculated by QM/MM approach displayed a notably low PT barrier (2.2 kcal/mol) and a dramatic energy difference (14.1 kcal/mol) in reactants versus immediate products, which implies that the proposed proton shuttle is concerted and energetically favorable. Our studies offer a reasonable pathway to yield a free base by assisting Lys78 deprotonation, thereby paving the way for future studies on Ser75 activation that is a critical step in catalysis by EstB, as well as biocatalyst development by rational attempts. This PT mode would also afford clues for the forthcoming investigation on acyltransferase LovD that is homologous to EstB.
资助项目	State Key Program of Basic Research of China ("973" Program)[2009CB918502] ; State Key Program of Basic Research of China ("973" Program)[2010CB732603] ; National Natural Science Foundation of China[20972174] ; National Natural Science Foundation of China[21021063] ; National Natural Science Foundation of China[30970712] ; National Natural Science Foundation of China[91029704] ; State Key Laboratory of Drug Research[SIMM1105KF-02] ; Shanghai Committee of Science and Technology[10410703900] ; Chinese Academy of Sciences[XDA01040305]
WOS关键词	GREEN FLUORESCENT PROTEIN ; MOLECULAR-ORBITAL METHOD ; C BETA-LACTAMASE ; GEOMETRY OPTIMIZATION ; DIRECTED EVOLUTION ; MODEL ; CONSTRAINTS ; DYNAMICS ; SYSTEM ; ONIOM
WOS研究方向	Chemistry
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000296394100040
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/278337]
专题	药物发现与设计中心中科院受体结构与功能重点实验室新药研究国家重点实验室
通讯作者	Wu, Daocheng
作者单位	1.Xi An Jiao Tong Univ, Key Lab Biomed Informat Engn, Minist Educ, Sch Life Sci & Technol, Xian 710049, Peoples R China; 2.Chinese Acad Sci, Drug Discovery & Design Ctr, State Key Lab Drug Res, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China; 3.Soochow Univ, Ctr Syst Biol, Suzhou 215006, Jiangsu, Peoples R China
推荐引用方式 GB/T 7714	Chen, Liang,Kong, Xiangqian,Liang, Zhongjie,et al. Theoretical Study of the Mechanism of Proton Transfer in the Esterase Estb from Burkholderia Gladioli[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2011,115(44):13019-13025.
APA	Chen, Liang.,Kong, Xiangqian.,Liang, Zhongjie.,Ye, Fei.,Yu, Kunqian.,...&Jiang, Hualiang.(2011).Theoretical Study of the Mechanism of Proton Transfer in the Esterase Estb from Burkholderia Gladioli.JOURNAL OF PHYSICAL CHEMISTRY B,115(44),13019-13025.
MLA	Chen, Liang,et al."Theoretical Study of the Mechanism of Proton Transfer in the Esterase Estb from Burkholderia Gladioli".JOURNAL OF PHYSICAL CHEMISTRY B 115.44(2011):13019-13025.