Structural Insight into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues,
- 22 July 2010
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 49 (35), 7683-7693
- https://doi.org/10.1021/bi100458d
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the final and rate-limiting step in methane biogenesis: the reduction of methyl-coenzyme M (methyl-SCoM) by coenzyme B (CoBSH) to methane and a heterodisulfide (CoBS-SCoM). Crystallographic studies show that the active site is deeply buried within the enzyme and contains a highly reduced nickel-tetrapyrrole, coenzyme F430. Methyl-SCoM must enter the active site prior to CoBSH, as species derived from methyl-SCoM are always observed bound to the F430 nickel in the deepest part of the 30 Å long substrate channel that leads from the protein surface to the active site. The seven-carbon mercaptoalkanoyl chain of CoBSH binds within a 16 Å predominantly hydrophobic part of the channel close to F430, with the CoBSH thiolate lying closest to the nickel at a distance of 8.8 Å. It has previously been suggested that binding of CoBSH initiates catalysis by inducing a conformational change that moves methyl-SCoM closer to the nickel promoting cleavage of the C−S bond of methyl-SCoM. In order to better understand the structural role of CoBSH early in the MCR mechanism, we have determined crystal structures of MCR in complex with four different CoBSH analogues: pentanoyl, hexanoyl, octanoyl, and nonanoyl derivatives of CoBSH (CoB5SH, CoB6SH, CoB8SH, and CoB9SH, respectively). The data presented here reveal that the shorter CoB5SH mercaptoalkanoyl chain overlays with that of CoBSH but terminates two units short of the CoBSH thiolate position. In contrast, the mercaptoalkanoyl chain of CoB6SH adopts a different conformation, such that its thiolate is coincident with the position of the CoBSH thiolate. This is consistent with the observation that CoB6SH is a slow substrate. A labile water in the substrate channel was found to be a sensitive indicator for the presence of CoBSH and HSCoM. The longer CoB8SH and CoB9SH analogues can be accommodated in the active site through exclusion of this water. These analogues react with Ni(III)-methyl, a proposed MCR catalytic intermediate of methanogenesis. The CoB8SH thiolate is 2.6 Å closer to the nickel than that of CoBSH, but the additional carbon of CoB9SH only decreases the nickel thiolate distance a further 0.3 Å. Although the analogues do not induce any structural changes in the substrate channel, the thiolates appear to preferentially bind at two distinct positions in the channel, one being the previously observed CoBSH thiolate position and the other being at a hydrophobic annulus of residues that lines the channel proximal to the nickel.Keywords
This publication has 49 references indexed in Scilit:
- Geometric and Electronic Structures of the NiI and Methyl−NiIII Intermediates of Methyl-Coenzyme M ReductaseBiochemistry, 2009
- Characterization of Alkyl-Nickel Adducts Generated by Reaction of Methyl-Coenzyme M Reductase with Brominated AcidsBiochemistry, 2007
- Coot: model-building tools for molecular graphicsActa crystallographica. Section D, Structural biology, 2004
- Spectroscopic investigation of the nickel-containing porphinoid cofactor F430. Comparison of the free cofactor in the +1, +2 and +3 oxidation states with the cofactor bound to methyl-coenzyme M reductase in the silent, red and ox formsJBIC Journal of Biological Inorganic Chemistry, 2004
- X-ray Absorption and Resonance Raman Studies of Methyl-Coenzyme M Reductase Indicating That Ligand Exchange and Macrocycle Reduction Accompany Reductive ActivationJournal of the American Chemical Society, 2002
- The nickel enzyme methyl-coenzyme M reductase from methanogenic archaea: In vitro induction of the nickel-based MCR-ox EPR signals from MCR-red2JBIC Journal of Biological Inorganic Chemistry, 2002
- Cryoreduction of Methyl-Coenzyme M Reductase: EPR Characterization of Forms, MCRox1 and MCRred1Journal of the American Chemical Society, 2001
- On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate bindingJournal of Molecular Biology, 2001
- The CCP4 suite: programs for protein crystallographyActa crystallographica. Section D, Structural biology, 1994
- Presence of nickel in Factor F430 from MethanobacteriumbryantiiBiochemical and Biophysical Research Communications, 1980