title: A realistic in silico model for structure/function studies of molybdenum-copper CO dehydrogenase.
abstract: CO dehydrogenase (CODH) is an environmentally crucial bacterial enzyme that oxidizes CO to CO2 at a Mo-Cu active site. Despite the close to atomic resolution structure (1.1 Å), significant uncertainties have remained with regard to the protonation state of the water-derived equatorial ligand coordinated at the Mo-center, as well as the nature of intermediates formed during the catalytic cycle. To address the protonation state of the equatorial ligand, we have developed a realistic in silico QM model (~179 atoms) containing structurally essential residues surrounding the active site. Using our QM model, we examined each plausible combination of redox states (Mo(VI)-Cu(I), Mo(V)-Cu(II), Mo(V)-Cu(I), and Mo(IV)-Cu(I)) and Mo-coordinated equatorial ligands (O(2-), OH(-), H2O), as well as the effects of second-sphere residues surrounding the active site. Herein, we present a refined computational model for the Mo(VI) state in which Glu763 acts as an active site base, leading to a MoO2-like core and a protonated Glu763. Calculated structural and spectroscopic data (hyperfine couplings) are in support of a MoO2-like core in agreement with XRD data. The calculated two-electron reduction potential (E = -467 mV vs. SHE) is in reasonable agreement with the experimental value (E = -558 mV vs. SHE) for the redox couple comprising an equatorial oxo ligand and protonated Glu763 in the Mo(VI)-Cu(I) state and an equatorial water in the Mo(IV)-Cu(I) state. We also suggest a potential role of second-sphere residues (e.g., Glu763, Phe390) based on geometric changes observed upon exclusion of these residues in the most plausible oxidized states.
authors.affiliation: Department of Chemistry, Whitman College, Walla Walla, WA, 99362, USA. rokhsad@whitman.edu.
authors.forename: Dalia
authors.initials: D
authors.lastname: Rokhsana
authors.affiliation: Department of Chemistry, Whitman College, Walla Walla, WA, 99362, USA.
authors.forename: Tao A G
authors.initials: TA
authors.lastname: Large
authors.affiliation: Department of Chemistry, Whitman College, Walla Walla, WA, 99362, USA.
authors.forename: Morgan C
authors.initials: MC
authors.lastname: Dienst
authors.affiliation: Max Planck Institute for Chemical Energy Conversion, 45470, Mülheim an der Ruhr, Germany.|European Synchrotron Radiation Facility, BP 220, 38043, Grenoble Cedex, France.
authors.forename: Marius
authors.initials: M
authors.lastname: Retegan
authors.affiliation: Max Planck Institute for Chemical Energy Conversion, 45470, Mülheim an der Ruhr, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Neese
mesh_terms: D000445:Aldehyde Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D020561:Alphaproteobacteria / Q000201:enzymology; D003198:Computer Simulation; D003300:Copper / Q000737:chemistry* / Q000378:metabolism; D008982:Molybdenum / Q000737:chemistry* / Q000378:metabolism; D009097:Multienzyme Complexes / Q000737:chemistry* / Q000378:metabolism; D011789:Quantum Theory
chemical_list: D009097:Multienzyme Complexes; D003300:Copper; D008982:Molybdenum; D000445:Aldehyde Oxidoreductases; C019823:carbon monoxide dehydrogenase
keywords: CO dehydrogenase; Computational model; Density functional theory; Molybdenum–copper bimetallic site; Quantum mechanics