The catalytic mechanism for aerobic formation of methane by bacteria
The catalytic mechanism for aerobic formation of methane by bacteria
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DOI：
10.1038/nature12061
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发表时间：
2013-05-02
期刊：
影响因子：
64.8
通讯作者：
Raushel, Frank M.
中科院分区：
文献类型：
--
作者：
Kamat, Siddhesh S.;Williams, Howard J.;Raushel, Frank M.
甲烷是一种强效温室气体，由有氧海洋生物大量产生（1）。这些细菌显然通过甲基膦酸酯（MPn）中高度不反应的碳-磷键的裂解催化甲烷的形成，但这种化合物的生物或陆地来源尚不清楚（2）。然而，海洋细菌Nitrosopumilus maritimus催化MPn从2-羟乙基膦酸酯的生物合成（3），并且已知细菌C-P裂解酶复合物将MPn转化为甲烷（4-7）。除了MPn之外，当磷酸盐的环境浓度低时，细菌C-P裂解酶复合物催化许多烷基膦酸酯的C-P键裂解（4-7）。来自C-P裂解酶复合物的PhnJ催化核糖-1-膦酸酯-5-磷酸至甲烷和核糖-1，2-环状-磷酸-5-磷酸的前所未有的C-P键裂解反应。该反应需要具有氧化还原活性的[4 Fe-4S]-簇和S-腺苷-L-甲硫氨酸，后者被还原切割为L-甲硫氨酸和5 '-脱氧腺苷（8）。在这里，我们表明，PhnJ是一种新的自由基S-腺苷-L-甲硫氨酸酶，催化C-P键裂解，通过最初形成的5 '-脱氧腺苷自由基和两个蛋白质为基础的自由基定位在Gly 32和Cys 272。在该转化过程中，来自Gly 32的pro-R氢被转移到5 '-脱氧腺苷自由基以形成5'-脱氧腺苷，而pro-S氢被转移到最终产生甲烷的自由基中间体。提出了一个全面的反应机理C-P键裂解的C-P裂解酶复合物，使用共价硫代磷酸中间体的甲烷和磷酸盐的形成。
Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms(1). These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon-phosphorus bond inmethylphosphonate(MPn), but the biological or terrestrial source of this compound is unclear(2). However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate(3) and the bacterial C-P lyase complex is known to convert MPn to methane(4-7). In addition to MPn, the bacterial C-P lyase complex catalyses C-P bond cleavage of many alkyl phosphonates when the environmental concentration of phosphate is low(4-7). PhnJ from the C-P lyase complex catalyses an unprecedented C-P bond cleavage reaction of ribose-1-phosphonate-5-phosphate to methane and ribose-1,2-cyclic-phosphate-5-phosphate. This reaction requires a redox-active [4Fe-4S]-cluster and S-adenosyl-L-methionine, which is reductively cleaved to L-methionine and 5'-deoxyadenosine(8). Here we show that PhnJ is a novel radical S-adenosyl-L-methionine enzyme that catalyses C-P bond cleavage through the initial formation of a 5'-deoxyadenosyl radical and two protein-based radicals localized at Gly 32 and Cys 272. During this transformation, the pro-R hydrogen from Gly 32 is transferred to the 5'-deoxyadenosyl radical to form 5'-deoxyadenosine and the pro-S hydrogen is transferred to the radical intermediate that ultimately generates methane. A comprehensive reaction mechanism is proposed for cleavage of the C-P bond by the C-P lyase complex that uses a covalent thiophosphate intermediate for methane and phosphate formation.