The crystal structure of methanogen McrD, a methyl-coenzyme M reductase-associated protein

Abstract

Methyl-coenzyme M reductase (MCR) is a multi-subunit (α₂β₂γ₂) enzyme responsible for methane formation via its unique F₄₃₀ cofactor. The genes responsible for producing MCR (mcrA, mcrB and mcrG) are typically colocated with two other highly conserved genes mcrC and mcrD. We present here the high-resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin-like domain assembled into an α + β barrel-like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.

Keywords: Methanomassiliicoccus luminyensis; McrD; ferredoxin‐like; methanogen; methyl‐coenzyme M reductase.

Fig. 1

Orthogonal views of the M. luminyensis McrD dimer crystal structure in cartoon representation. Monomer A is sequence colour‐ramped from the N terminus (dark blue) to the C terminus (red) with secondary structure elements labelled. Monomer B is grey scale‐ramped from the N terminus (black) to the C terminus (light grey). N and C label the McrD N terminus (amino acid 1) and C terminus (amino acid 129/130), respectively.

Fig. 2

The McrD electron density across a region of the dimer interface. The McrD structure is shown in stick representation coloured by atom type; carbon atoms are coloured green or grey for monomer A and monomer B respectively, oxygen are red and nitrogen are blue. The weighted 2fo‐fc electron density is contoured at 1 sigma and clipped to the atoms shown at a radius of 1.5 Å.

Fig. 3

Superposition of the M. luminyensis (Ml) and M. acetivorans (Ma) McrD structures in cartoon representation. MlMcrD monomer A (Ml‐A) is colour‐ramped N to C terminus from blue to red, MlMcrD monomer B (Ml‐B) is grey scale‐ramped N to C termini black to light grey MaMcrD (Ma) (PDB: 8GF6) [15] is shown in purple. Loop 5 and the termini are labelled. The MlMcrD amino acids within the plasmid‐encoded affinity tag were not included in the superposition and are not shown.

Fig. 4

McrD ConSurf [40] sequence conservation analysis mapped on to the M. luminyensis McrD crystal structure. The dimer structure is shown in cartoon representation with monomer A colour‐ramped by sequence conservation as calculated from 150 sequences (dark magenta most conserved, white intermediate and cyan least conserved). Monomer B is coloured yellow. The N‐terminal plasmid tag‐encoded amino acids in the structure were removed for this analysis.