嗜热丁烷氧化古菌Candidatus Syntrophoarchaeum烷基转移酶MtaA催化丁基辅酶M的分子机制研究  

Molecular mechanism of the alkyl-transferase MtaA catalyzing butyl-CoM in the thermophilic butane-oxidizing archaea Candidatus Syntrophoarchaeum

作　　者：王瑾 田晓翩 李政新 陈海峰[1] 王风平[1] WANG Jin;TIAN Xiaopian;LI Zhengxin;CHEN Haifeng;WANG Fengping(State Key Laboratory of Microbial Metabolism,School of Life Sciences and Biotechnology,Shanghai Jiao Tong University,Shanghai 200240,China)

机构地区：[1]上海交通大学生命科学技术学院微生物代谢国家重点实验室,上海200240

出　　处：《微生物学通报》2021年第10期3401-3408,共8页Microbiology China

基　　金：国家重点研发计划(2018YFC0310803);国家自然科学基金(91751205,41867057)。

摘　　要：【背景】嗜热古菌Candidatus Syntrophoarchaeum可以与硫酸盐还原细菌共生,通过逆转产甲烷途径进行正丁烷的氧化,但在该过程中负责催化丁基辅酶M氧化的酶尚未确定。【目的】利用分子动力学模拟证明Ca.Syntrophoarchaeum中mta A基因编码的蛋白可以特异性催化丁基辅酶M中丁基的转移,并非转移甲基。【方法】使用Methanosarcina mazei辅酶M甲基转移酶Mta A的晶体结构(PDB ID:4ay8)作为模板,对Mta A_1 (Gen Bank登录号OFV65993.1)和Mta A_2 (Gen Bank登录号OFV65678.1)进行同源建模。使用分子对接得到两者分别结合CH3-Co M和C_(4)H_(9)-Co M时的结构,并用AMBER18进行分子动力学模拟。【结果】当Mta A_1和Mta A_2分别结合C_(4)H_(9)-Co M时,表现出与4ay8晶体结构类似的TIM-Barrel折叠三维结构,但在活性中心形状、Zn^(2+)与底物距离以及活性位点附近氨基酸配位方式等方面存在差异,这可能是导致Ca.Syntrophoarchaeum中mta A基因编码的蛋白催化丁基辅酶M氧化的原因。其中Mta A_2与4ay8结构更相似,活性中心氨基酸配位更完整,暗示其更可能具备催化活性。然而当Mta A_1和Mta A_2分别结合CH3-Co M时,整体结构不合实际,活性中心Zn^(2+)与底物距离过远,表明底物几乎不可能与酶结合。【结论】Ca.Syntrophoarchaeum中的Mta A_1和Mta A_2很可能是特异性的丁基转移酶,而非催化甲基的转移,其中Mta A_2具备活性的可能性更高。[Background]Thermophilic archaea Candidatus Syntrophoarchaeum was found to coexist with sulfate-reducing bacteria and oxidize n-butane by the reverse methanogenesis pathway.However,in this process,the enzyme responsible for catalyzing the oxidation of butyl-Co M has not been determined yet.[Objective]Using molecular dynamics simulation to prove that the enzymes encoded by mta A genes found in Ca.Syntrophoarchaeum can specifically catalyze the transfer of butyl in butyl-Co M,and they are not methyltransferases.[Methods]Using the crystal structure of Methanosarcina mazei coenzyme M methyltransferase Mta A (PDB ID:4ay8) as a template,homology modeling of Mta A_1 (Gen Bank ID:OFV65993.1) and Mta A_2 (Gen Bank ID:OFV65678.1) was performed.Molecular docking was used to obtain the structure when they were combined with CH3-Co M and C_(4)H_(9)-Co M respectively,and AMBER18was used for molecular dynamics simulation.[Results]When combined with C_(4)H_(9)-Co M,Mta A_1 and Mta A_2 exhibited a TIM-barrel-like three-dimensional structure similar to the fold of 4ay8.However,there are differences in the shape of the active site,the distance between Zn^(2+) and the substrate,and the coordination of amino acid residues around the active site.These differences may be the reason why the enzymes encoded by mta A genes found in Ca.Syntrophoarchaeum catalyze the oxidation of butyl-Co M.The overall structure of Mta A_2 is more similar to 4ay8,and the coordination of residues around the active site is complete,suggesting that Mta A_2 is more likely to be active.When Mta A_1 and Mta A_2bind to CH3-Co M respectively,their overall structures are unrealistic,and the coordinated Zn^(2+) is too far away from the substrate,indicating that CH3-Co M is almost impossible to bind to the enzyme.[Conclusion]Mta A_1 and Mta A_2 of Ca.Syntrophoarchaeum are likely to be specific butyl-transferases rather than catalyzing the transfer of methyl groups,and Mta A_2 is more likely to be active.

关 键 词：Candidatus Syntrophoarchaeum 丁烷厌氧氧化 烷基转移酶 分子动力学模拟 

分 类 号：Q936[生物学—微生物学]