A realistic in silico model for structure/function studies of molybdenum–copper CO dehydrogenase

  • Dalia RokhsanaEmail author
  • Tao A. G. Large
  • Morgan C. Dienst
  • Marius Retegan
  • Frank Neese
Original Paper


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 (MoVI–CuI, MoV–CuII, MoV–CuI, and MoIV–CuI) and Mo-coordinated equatorial ligands (O2−, 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 MoVI–CuI state and an equatorial water in the MoIV–CuI 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.


CO dehydrogenase Molybdenum–copper bimetallic site Density functional theory Quantum mechanics Computational model 



This research was funded by generous financial contributions from Whitman College and the M. J. Murdock Charitable Trust. Special thanks to Dr. Robert Szilagyi (Montana State University, Bozeman, MT) for his tremendous assistance in setting up the computational server at Whitman College, and for providing comments and feedback during the preparation of this manuscript. We gratefully acknowledge the Max Planck Society for financial support of this work.

Supplementary material

775_2016_1359_MOESM1_ESM.pdf (693 kb)
Supplementary material 1 (PDF 693 kb)
775_2016_1359_MOESM2_ESM.pdf (158 kb)
Supplementary material 2 (PDF 158 kb)


  1. 1.
    Mörsdorf G, Frunzke K, Gadkari D, Meyer O (1992) Biodegradation 3:61–82CrossRefGoogle Scholar
  2. 2.
    Moxley JM, Smith KA (1998) Soil Biol Biochem 30:65–79CrossRefGoogle Scholar
  3. 3.
    Wilcoxen J, Hille R (2013) J Biol Chem 288:36052–36060CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Dobbek H, Gremer L, Kiefersauer R, Huber R, Meyer O (2002) Proc Natl Acad Sci 99:15971–15976CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Gnida M, Ferner R, Gremer L, Meyer O, Meyer-Klaucke W (2003) Biochemistry 42:222–230CrossRefPubMedGoogle Scholar
  6. 6.
    Zhang B, Hemann CF, Hille R (2010) J Biol Chem 285:12571–12578CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Shanmugam M, Wilcoxen J, Habel-Rodriguez D, Cutsail GE 3rd, Kirk ML, Hoffman BM, Hille R (2013) J Am Chem Soc 135:17775–17782CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Siegbahn PE, Shestakov AF (2005) J Comput Chem 26:888–898CrossRefPubMedGoogle Scholar
  9. 9.
    Stein BW, Kirk ML (2015) J Biol Inorg Chem 20:183–194CrossRefPubMedGoogle Scholar
  10. 10.
    Neese F (2012) Wiley Interdiscip Rev Comput Mol Sci 2:73–78CrossRefGoogle Scholar
  11. 11.
    Klamt A, Schuurmann G (1993) J Chem Soc Perkin Trans 2:799–805CrossRefGoogle Scholar
  12. 12.
    Becke AD (1988) Phys Rev A 38:3098–3100CrossRefGoogle Scholar
  13. 13.
    Perdew JP (1986) Phys Rev B 33:8822–8824CrossRefGoogle Scholar
  14. 14.
    Bühl M, Kabrede H (2006) J Chem Theory Comput 2:1282–1290CrossRefPubMedGoogle Scholar
  15. 15.
    Pantazis DA, Chen X-Y, Landis CR, Neese F (2008) J Chem Theory Comput 4:908–919CrossRefPubMedGoogle Scholar
  16. 16.
    Neese F (2003) J Comput Chem 24:1740–1747CrossRefPubMedGoogle Scholar
  17. 17.
    Weigend F (2006) Phys Chem Chem Phys 8:1057–1065CrossRefPubMedGoogle Scholar
  18. 18.
    Bykov D, Petrenko T, Izsák R, Kossmann S, Becker U, Valeev E, Neese F (2015) Mol Phys 113:1961–1977CrossRefGoogle Scholar
  19. 19.
    Knizia G (2013) J Chem Theory Comput 9:4834–4843CrossRefPubMedGoogle Scholar
  20. 20.
    Becke AD (1993) J Chem Phys 98:5648–5652CrossRefGoogle Scholar
  21. 21.
    Staroverov VN, Scuseria GE, Tao J, Perdew JP (2003) J Chem Phys 119:12129–12137CrossRefGoogle Scholar
  22. 22.
    Izsak R, Neese F (2011) J Chem Phys 135:144105CrossRefPubMedGoogle Scholar
  23. 23.
    Neese F, Wennmohs F, Hansen A, Becker U (2009) Chem Phys 356:98–109CrossRefGoogle Scholar
  24. 24.
    Palascak MW, Shields GC (2004) J Phys Chem A 108:3692–3694CrossRefGoogle Scholar
  25. 25.
    Sinnecker S, Neese F (2006) J Comput Chem 27:1463–1475CrossRefPubMedGoogle Scholar
  26. 26.
    Rokhsana D, Dooley DM, Szilagyi RK (2008) J Biol Inorg Chem 13:371–383CrossRefPubMedGoogle Scholar
  27. 27.
    Bjornsson R, Lima FA, Spatzal T, Weyhermuller T, Glatzel P, Bill E, Einsle O, Neese F, DeBeer S (2014) Chem Sci 5:3096–3103CrossRefGoogle Scholar
  28. 28.
    Gourlay C, Nielsen DJ, White JM, Knottenbelt SZ, Kirk ML, Young CG (2006) J Am Chem Soc 128:2164–2165CrossRefPubMedGoogle Scholar
  29. 29.
    Hille R, Dingwall S, Wilcoxen J (2015) J Biol Inorg Chem 20:243–251CrossRefPubMedGoogle Scholar

Copyright information

© SBIC 2016

Authors and Affiliations

  • Dalia Rokhsana
    • 1
    Email author
  • Tao A. G. Large
    • 1
  • Morgan C. Dienst
    • 1
  • Marius Retegan
    • 2
    • 3
  • Frank Neese
    • 2
  1. 1.Department of ChemistryWhitman CollegeWalla WallaUSA
  2. 2.Max Planck Institute for Chemical Energy ConversionMülheim an der RuhrGermany
  3. 3.European Synchrotron Radiation FacilityGrenoble CedexFrance

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