Structural basis for methylphosphonate biosynthesis

Abstract

Methylphosphonate synthase (MPnS) produces methylphosphonate, a metabolic precursor to methane in the upper ocean. Here we determine a 2.35-Å 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.

How To Produce Methane Precursor in the Upper Ocean by An Untypical Non‐Heme Fe‐Dependent Methylphosphonate Synthase?

“…A chemical model of the active site of MPnS (Figure ) was constructed on the basis of an X‐ray crystal structure of MPnS together with the substrate 2‐HEP (PDB code: 6B9T) . The crystal structure used here truly reflects the enzyme‐substrate positions and must be a reasonable initial geometry for the modelling.…”

“…The X-ray crystal structure of MPnS (PDB code 6B9T). [17] A) A monomer of MPnS consisting of four domains (α1, α2, β1, and β2). B) Overall view of the dimer of MPnS and close-up view of the active site.…”

“…The iron is shown as a magenta sphere and water molecule is referred to as W. together with the substrate 2-HEP (PDB code: 6B9T). [17] The crystal structure used here truly reflects the enzyme-substrate positions and must be a reasonable initial geometry for the modelling. The model consists of an Fe(II) ion, the first-shell ligands (His190, His148, Gln152, a 2-HEP substrate, and an dioxygen molecule which replaces the original water molecule), and six second-shell residues (Thr154, Tyr110, Arg102, Asn145, Lys28', and Trp449').…”

“…[17] There are two active sites in MPnS, each of which consists of a ferrous iron, seven residues from the β1 domain (His190, His148, Gln152, Thr154, Tyr110, Arg102, and Asn145) and two residues from the α1' domain located at another monomer (Lys28' and Trp449') ( Figure 2B). [17] The Fe(II) ion is hexacoordinated by a water, the hydroxyl and phosphoryl of the substrate (2-HEP), His190, His148, and Gln152 ( Figure 2B). Such an Fe coordination mode composed of two histidines and one glutamine (2-His-1-Gln) is uncommon in MNHFe enzymes, which usually possess the 2-His-1-carboxylate (Glu or Asp) or 3-His motif coordination (so-called "facial triad"), a canonical character for MNHFe enzymes.…”

Controls on zooplankton methane production in the central Baltic Sea

“…populations as critical participants in this methanogenic pathway (Wang et al, 2017). MPn was shown to be ubiquitous in dissolved organic matter in the ocean (Repeta et al, 2016), and the MPn biosynthetic key enzyme was identified in the archaeon Nitrosopumilus maritimus and the α-proteobacteria Pelagibacter ubique, two of the most abundant marine prokaryotes (Metcalf et al, 2012;Born et al, 2017). 20 (II) Studies conducted at Lake Stechlin (Germany) suggest a model in which methane production is related to the activity of hydrogenotrophic methanogens attached to photoautotrophs (Grossart et al, 2011).…”