Can the local enzyme scaffold act as an H-donor for a Co(I)H bond formation? The curious case of methionine synthase-bound cob(I)alamin

J Inorg Biochem. 2013 Sep:126:26-34. doi: 10.1016/j.jinorgbio.2013.04.009. Epub 2013 Apr 30.

Abstract

The density functional calculations and analysis of the existing X-ray crystallographic data have been carried out to gain mechanistic insight into the reactivation cycle of methionine synthase (MetH) enzyme. The calculations were carried out on the cobinamide-type model complexes of cob(I)alamin (Co(I)Cbx) testing H2O and PhOH as possible β-axial ligands. The PhOH motif was used to mimic the tyrosine (Y1139) residue that has been found in the active site of the MetH-bound cob(II)alamin (Co(II)Cbx). The calculations indicate that the β-axial PhOH ligand forms stronger Co(I)H bonds than H2O ligand due to its better H-donor capacity. The calculated redox tuning of Co(I)H interactions on the reduction potential of Co(II)/Co(I) couple (60-800 mV vs standard hydrogen electrode (SHE)), irrespective of the β-axial ligand considered, is significantly higher than the biological redox gap between the reduction potential of Co(II)/Co(I) couple and that of the biological reducing agents (50 mV vs SHE). The analysis of existing crystallographic data for the reactivation conformation of MetH enzyme (1K7Y (@3.0 Å); 1K98 (@3.8 Å) and 3IVA (@2.7 Å)) indicates that the Y1139 residue and the β-axial H2O ligand in the MetH-bound Co(II)Cbx complex are equidistant from the Co(II) ion (Y1139Co(II)=3.97 Å; H2OCo(II)=3.96 Å). Taking into account that the Y1139-induced Co(I)H linkages are thermodynamically more stable than the H2O-induced ones, the present calculations suggest that the Y1139 residue may serve as the β-axial ligand in the reactivation conformation of MetH enzyme.

Keywords: Co(I)H interaction; Co(II)/Co(I) reduction; Cob(I)alamin; Methionine synthase.

MeSH terms

  • 5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase / chemistry*
  • Bacterial Proteins / chemistry*
  • Biocatalysis
  • Catalytic Domain
  • Cations, Monovalent
  • Cobalt / chemistry*
  • Cobamides / chemistry*
  • Crystallography, X-Ray
  • Electron Spin Resonance Spectroscopy
  • Escherichia coli / chemistry*
  • Escherichia coli / enzymology
  • Kinetics
  • Ligands
  • Models, Molecular
  • Oxidation-Reduction
  • Protons*
  • Quantum Theory
  • Thermodynamics
  • Tyrosine / chemistry
  • Water / chemistry

Substances

  • Bacterial Proteins
  • Cations, Monovalent
  • Cobamides
  • Ligands
  • Protons
  • Water
  • cobinamide
  • Cobalt
  • Tyrosine
  • 5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase