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Structural basis for methylphosphonate biosynthesis

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Science  08 Dec 2017:
Vol. 358, Issue 6368, pp. 1336-1339
DOI: 10.1126/science.aao3435

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A source of methane in the upper ocean

Methane concentrations are high in oxygenated surface waters. Methylphosphonate (MPn) is a suggested source, but an enzyme that synthesizes Mpn (MPnS) has so far only been identified in one ocean microbe, albeit an abundant one: the archaeon Nitrosopumilus maritimus. Born et al. describe the crystal structure of MPnS and of a related enzyme that acts on the same substrate but makes a different product. By comparing the structures, they determined sequence markers that allowed them to identify MPnS in other ocean microbes, including the abundant microbe Pelagibacter ubique. These findings support the proposal that MPn is a source of both methane and phosphorus in the upper aerobic ocean.

Science, this issue p. 1336

Abstract

Methylphosphonate synthase (MPnS) produces methylphosphonate, a metabolic precursor to methane in the upper ocean. Here, we determine a 2.35-angstrom resolution structure of MPnS and discover that it has an unusual 2-histidine-1-glutamine iron-coordinating triad. We further solve the structure of a related enzyme, hydroxyethylphosphonate dioxygenase from Streptomyces albus (SaHEPD), and find that it displays the same motif. SaHEPD can be converted into an MPnS by mutation of glutamine-adjacent residues, identifying the molecular requirements for methylphosphonate synthesis. Using these sequence markers, we find numerous putative MPnSs in marine microbiomes and confirm that MPnS is present in the abundant Pelagibacter ubique. The ubiquity of MPnS-containing microbes supports the proposal that methylphosphonate is a source of methane in the upper, aerobic ocean, where phosphorus-starved microbes catabolize methylphosphonate for its phosphorus.

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