Insights into the catalytic mechanism of dehydrogenase BphB: A quantum mechanics/molecular mechanics study
Insights into the catalytic mechanism of dehydrogenase BphB: A quantum mechanics/molecular mechanics study
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深入了解脱氢酶 BphB 的催化机制：量子力学/分子力学研究
DOI：
10.1016/j.chemosphere.2018.05.063
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发表时间：
2018
期刊：
影响因子：
8.8
通讯作者：
Wang Wenxing
中科院分区：
文献类型：
--
作者：
Zhang Ruiming;Shi Xiangli;Sun Yanhui;Zhang Qingzhu;Wang Wenxing
本研究详细描述了顺式2,3-二氢-2,3-二羟基联苯（2,3- ddbph）和顺式2,3-二氢-2,3-二羟基-4,4 ' -二氯联苯（2,3- dd -4,4 ' -DBPH）在andoraea现象菌株b - 356顺式2,3-二氢-2,3- 2,3-二羟基联苯脱氢酶（BphB）中的脱氢机理。采用量子力学/分子力学（QM/MM）相结合的方法研究了酶促过程。提取并计算了5种不同的快照，结果表明2,3- ddbph和2,3- dd -4,4 ' -DBPH脱氢过程的boltzmann加权平均势垒分别为10.7和11.5 kcal mol−1。建立的脱氢机理为其他氯化2,3- ddbph的降解过程提供了新的认识。除了Asn115、Ser142和Lys149外，还重点研究了Ile 89、Asn143、Pro184、Met 187、Thr189和Lue 191在2,3- ddbph和2,3- dd -4,4 ' -DBPH脱氢过程中的重要性，以寻找提高BphB催化效率的有希望的突变靶点。
The present study delineated the dehydrogenation mechanism ofcis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) andcis-2,3-dihydro-2,3-dihydroxy-4,4′-dichlorobiphenyl (2,3-DD-4,4′-DBPH) byPandoraea pnomenusastrain B-356cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) in atomistic detail. The enzymatic process was investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Five different snapshots were extracted and calculated, which revealed that the Boltzmann-weighted average barriers of 2,3-DDBPH and 2,3-DD-4,4′-DBPH dehydrogenation processes are 10.7 and 11.5 kcal mol−1, respectively. The established dehydrogenation mechanism provides new insight into the degradation processes of other chlorinated 2,3-DDBPH. In addition to Asn115, Ser142, and Lys149, the importance of Ile 89, Asn143, Pro184, Met 187, Thr189, and Lue 191 during the dehydrogenation process of 2,3-DDBPH and 2,3-DD-4,4′-DBPH were also highlighted to search for promising mutation targets for improving the catalytic efficiency of BphB.