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The catalytic mechanism for aerobic formation of methane by bacteria


Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms1. These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon–phosphorus bond in methyl phosphonate (MPn), but the biological or terrestrial source of this compound is unclear2. However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate3 and the bacterial C–P lyase complex is known to convert MPn to methane4,5,6,7. 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 low4,5,6,7. 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′-deoxyadenosine8. 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.

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Figure 1: EPR spectra of wild-type PhnJ and the Cys272Ala mutant.
Figure 2: Mass spectra of 5′-deoxyadenosine and methane from reactions catalysed by PhnJ.
Figure 3: Identification of Gly 32 as the site of the glycyl radical.
Figure 4: Proposed mechanism for the reaction catalysed by PhnJ.
Figure 5: 31P-NMR spectrum of tryptic fragments of PhnJ after reaction with 2-dPRPn.

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We thank D. Barondeau for use of the anaerobic chamber, R. Stipanovic for use of the gas chromatography mass spectrometer, A. Mehta and T. Begley for use of the liquid chromatography mass spectrometer, and C. Hilty for use of the 31P-NMR spectrometer. We thank P. A. Lindahl for help with the EPR measurements (GM084266). This work was supported by the Robert A. Welch Foundation (A-840).

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S.S.K., H.J.W. and F.M.R. designed the experiments. S.S.K. did the cloning and purification, performed the reactions and made all samples for analysis. S.S.K. and H.J.W. did the NMR, gas chromatography and gas chromatography mass spectrometry experiments. M.C. collected and analysed the EPR data. S.S.K. and L.J.D. did the trypsin digestion and peptide analysis. The manuscript was written by S.S.K. and F.M.R.

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Correspondence to Frank M. Raushel.

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The authors declare no competing financial interests.

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Kamat, S., Williams, H., Dangott, L. et al. The catalytic mechanism for aerobic formation of methane by bacteria. Nature 497, 132–136 (2013).

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