title: The catalytic mechanism for aerobic formation of methane by bacteria.
abstract: Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms. 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 unclear. However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate and the bacterial C-P lyase complex is known to convert MPn to methane. 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. 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. 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.
authors.affiliation: Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA.
authors.forename: Siddhesh S
authors.initials: SS
authors.lastname: Kamat
authors.forename: Howard J
authors.initials: HJ
authors.lastname: Williams
authors.forename: Lawrence J
authors.initials: LJ
authors.lastname: Dangott
authors.forename: Mrinmoy
authors.initials: M
authors.lastname: Chakrabarti
authors.forename: Frank M
authors.initials: FM
authors.lastname: Raushel
mesh_terms: D000332:Aerobiosis; D001105:Archaea / Q000378:metabolism; D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D055162:Biocatalysis; D003839:Deoxyadenosines / Q000737:chemistry / Q000378:metabolism; D004578:Electron Spin Resonance Spectroscopy; D005998:Glycine / Q000737:chemistry / Q000378:metabolism; D006859:Hydrogen / Q000378:metabolism; D008190:Lyases / Q000737:chemistry / Q000378:metabolism; D013058:Mass Spectrometry; D008697:Methane / Q000096:biosynthesis* / Q000737:chemistry / Q000378:metabolism; D008715:Methionine / Q000378:metabolism; D050505:Mutant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010428:Pentosephosphates / Q000737:chemistry / Q000378:metabolism; D012436:S-Adenosylmethionine / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D003839:Deoxyadenosines; D050505:Mutant Proteins; D010428:Pentosephosphates; D012436:S-Adenosylmethionine; D006859:Hydrogen; D008715:Methionine; D008190:Lyases; D008697:Methane; D005998:Glycine