Journal of Microbiology

, Volume 56, Issue 4, pp 246–254 | Cite as

The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT

  • Thinh-Phat Cao
  • Jin Myung Choi
  • Si Wouk Kim
  • Sung Haeng Lee
Microbial Physiology and Biochemistry


The first crystal structure of a pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) from a marine methylotrophic bacterium, Methylophaga aminisulfidivorans MPT (MDHMas), was determined at 1.7 Å resolution. The active form of MDHMas (or MDHIMas) is a heterotetrameric α2β2, where each β-subunit assembles on one side of each of the α-subunits, in a symmetrical fashion, so that two β-subunits surround the two PQQ-binding pockets on the α-subunits. The active site consists of a PQQ molecule surrounded by a β-propeller fold for each α-subunit. Interestingly, the PQQ molecules are coordinated by a Mg2+ ion, instead of the Ca2+ ion that is commonly found in the terrestrial MDHI, indicating the efficiency of osmotic balance regulation in the high salt environment. The overall interaction of the β-subunits with the α-subunits appears tighter than that of terrestrial homologues, suggesting the efficient maintenance of MDHIMas integrity in the sea water environment to provide a firm basis for complex formation with MxaJMas or Cyt cL. With the help of the features mentioned above, our research may enable the elucidation of the full molecular mechanism of methanol oxidation by taking advantage of marine bacterium-originated proteins in the methanol oxidizing system (mox), including MxaJ, as the attainment of these proteins from terrestrial bacteria for structural studies has not been successful.


methanol dehydrogenase methanol oxidizing system pyrroloquinoline quinone Mg2+ marine bacterium 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

12275_2018_7483_MOESM1_ESM.pdf (1.7 mb)
Supplementary material, approximately 1.65 MB.


  1. Abergel, C. 2013. Molecular replacement: Tricks and treats. Acta Crystallogr. D Biol. Crystallogr. 69, 2167–2173.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Anthony, C. 1986. Bacterial oxidation of methane and methanol. Adv. Microb. Physiol. 27, 113–210.CrossRefPubMedGoogle Scholar
  4. Anthony, C. 1996. Quinoprotein-catalysed reactions. Biochem. J. 320, 697–711.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Anthony, C., Ghosh, M., and Blake, C.C.F. 1994. The structure and function of methanol dehydrogenase and related quinoproteins containing pyrrolo-quinoline quinone. Biochem. J. 304, 665–674.CrossRefPubMedPubMedCentralGoogle Scholar
  6. Archer, D., Buffett, B., and Brovkin, V. 2008. Ocean methane hydrates as a slow tipping point in the global carbon cycle. Proc. Natl. Acad. Sci. USA 106, 20596–20601.CrossRefPubMedGoogle Scholar
  7. Baker, N.A., Sept, D., Joseph, S., Holst, M.J., and McCammon, J.A. 2001. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037–10041.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Blake, C.C.F., Ghosh, M., Harlos, K., Avezoux, A., and Anthony, C. 1994. The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues. J. Struct. Biol. 1, 102–105.CrossRefGoogle Scholar
  9. Chen, V.B., Arendall, W.B., Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., and Richardson, D.C. 2009. Molprobity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Choi, J.M., Cao, T.P., Kim, S.W., Lee, K.H., and Lee, S.H. 2017. MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements. Proteins 85, 1379–1386.CrossRefGoogle Scholar
  11. Choi, J.M., Kim, H.G., Kim, J.S., Youn, H.S., Eom, S.H., Yu, S.L., Kim, S.W., and Lee, S.H. 2011. Purification, crystallization and preliminary X-ray crystallographic analysis of a methanol dehydrogenase from the marine bacterium Methylophaga aminisulfidivorans MPT. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67, 513–516.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Culkin, F. 1965. The major constituents of sea water, pp. 121–161. In Riley, J.P. and Skirrow, G. (eds.), Chemical oceanography, First Academic Press, New York, USA.Google Scholar
  13. Culpepper, M.A. and Rosenzweig, A.C. 2014. Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 53, 6211–6219.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Echols, N., Moriarty, N.W., Klei, H.E., Afonine, P.V., Bunkóczi, G., Headd, J.J., McCoy, A.J., Oeffner, R.D., Read, R.J., Terwilliger, T.C., et al. 2013. Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 70, 144–154.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Edgar, R.C. 2004. Muscle multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797.CrossRefPubMedPubMedCentralGoogle Scholar
  16. Emsley, P., Lohkamp, B., Scott, W.G., and Cowtan, K. 2010. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501.CrossRefPubMedPubMedCentralGoogle Scholar
  17. Ghosh, M., Anthony, C., Harlos, K., Goodwin, M.G., and Blake, C. 1995. The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 Å. Structure 15, 177–187.CrossRefGoogle Scholar
  18. Halevy, I. and Bachan, A. 2017. The geologic history of seawater pH. Science 355, 1069–1071.CrossRefPubMedGoogle Scholar
  19. Harris, T.K. and Davidson, V.L. 1994. Replacement of enzymebound calcium with strontium alters the kinetic properties of methanol dehydrogenase. Biochem. J. 300, 175–182.CrossRefPubMedPubMedCentralGoogle Scholar
  20. Haynes, C.A. and Gonzalez, R. 2014. Rethinking biological activation of methane and conversion to liquid fuels. Nat. Chem. Biol. 10, 331–339.CrossRefPubMedGoogle Scholar
  21. Heldal, M., Norland, S., Erichsen, E.S., Sandaa, R.A., Larsen, A., Thingstad, F., and Bratbak, G. 2011. Mg2+ as an indicator of nutritional status in marine bacteria. ISME J. 6, 524–530.CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kester, D.R., Duedall, I.W., Connors, D.N., and Pytkowicz, R.M. 1967. Preparation of artificial seawater. Limnol. Oceanogr. 12, 176–179.CrossRefGoogle Scholar
  23. Kim, H.G., Doronina, N.V., Trotsenko, Y.A., and Kim, S.W. 2007. Methylophaga aminisulfidivorans sp. nov., a restricted facultatively methylotrophic marine bacterium. Int. J. Syst. Evol. Microbiol. 57, 2096–2101.CrossRefPubMedGoogle Scholar
  24. Kim, H.G., Han, G.H., Kim, D., Choi, J.S., and Kim, S.W. 2012. Comparative analysis of two types of methanol dehydrogenase from Methylophaga aminisulfidivorans MPT grown on methanol. J. Basic Microbiol. 52, 141–149.CrossRefPubMedGoogle Scholar
  25. Knittel, K. and Boetius, A. 2009. Anaerobic oxidation of methane: Progress with an unknown process. Annu. Rev. Microbiol. 63, 311–334.CrossRefPubMedGoogle Scholar
  26. Li, J., Gan, J.H., Mathews, F.S., and Xia, Z.X. 2011. The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase. Biochem. Biophys. Res. Commun. 406, 621–626.CrossRefPubMedGoogle Scholar
  27. Marion, G.M., Millero, F.J., Camões, M.F., Spitzer, P., Feistel, R., and Chen, C.T.A. 2011. pH of seawater. Mar. Chem. 126, 89–96.Google Scholar
  28. Murshudov, G.N., Vagin, A.A., and Dodson, E.J. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta. Crystallogr. D Biol. Crystallogr. 53, 240–255.CrossRefPubMedGoogle Scholar
  29. Nojiri, M., Hira, D., Yamaguchi, K., Okajima, T., Tanizawa, K., and Suzuki, S. 2006. Crystal structures of cytochrome cL and methanol dehydrogenase from Hyphomicrobium denitrificans: Structural and mechanistic insights into interactions between the two proteins. Biochemistry 45, 3481–3492.CrossRefPubMedGoogle Scholar
  30. Olsson, M.H.M., Søndergaard, C.R., Rostkowski, M., and Jensen, J.H. 2011. PROPKA3 consistent treatment of internal and surface residues in empirical pKa predictions. J. Chem. Theory Comput. 7, 525–537.CrossRefPubMedGoogle Scholar
  31. Pol, A., Barends, T.R.M., Dietl, A., Khadem, A.F., Eygensteyn, J., Jetten, M.S.M., and Op den Camp, H.J.M. 2014. Rare earth metals are essential for methanotrophic life in volcanic mudpots. Environ. Microbiol. 16, 255–264.CrossRefPubMedGoogle Scholar
  32. Spanning, R.J.M.V., Wansell, C.W., Boer, T.D., Hazelaar, M.J., Anazawa, H., Harms, N., Oltmann, L.F., and Stouthamer, A.H. 1991. Isolation and characterization of the moxJ, moxG, moxI, and moxR genes of Paracoccus denitrificans: Inactivation of moxJ, moxG, and moxR and the resultant effect on methylotrophic growth. J. Bacteriol. 173, 6948–6961.CrossRefPubMedPubMedCentralGoogle Scholar
  33. Suplatov, D., Kirilin, E., Takhaveev, V., and Švedas, V. 2013a. Zebra: A web server for bioinformatic analysis of diverse protein families. J. Biomol. Struct. Dyn. 32, 1752–1758.CrossRefPubMedGoogle Scholar
  34. Suplatov, D., Shalaeva, D., Kirilin, E., Arzhanik, V., and Švedas, V. 2013b. Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity. J. Biomol. Struct. Dyn. 32, 75–87.CrossRefPubMedGoogle Scholar
  35. Williams, P.A., Coates, L., Mohammed, F., Gill, R., Erskine, P.T., Coker, A., Wood, S.P., Anthony, C., and Cooper, J.B. 2004. The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens. Acta Crystallogr. D. Biol. Crystallogr. 61, 75–79.CrossRefPubMedGoogle Scholar
  36. Xia, Z.X., Dai, W.W., He, Y.N., White, S.A., Mathews, F.S., and Davidson, V.L. 2003. X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i. J. Biol. Inorg. Chem. 8, 843–854.CrossRefPubMedGoogle Scholar
  37. Xia, Z.X., Dai, W.W., Zhang, Y.F., White, S.A., Boyd, G.D., and Mathews, F.S. 1996. Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1. J. Mol. Biol. 259, 480–501.CrossRefPubMedGoogle Scholar
  38. Zheng, Y.J. and Bruice, T.C. 1997. Conformation of coenzyme pyrroloquinoline quinone and role of Ca2+ in the catalytic mechanism of quinoprotein methanol-dehydrogenase. Proc. Natl. Acad. Sci. USA 94, 11881–11886.CrossRefPubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer Nature B.V. 2018

Authors and Affiliations

  • Thinh-Phat Cao
    • 1
  • Jin Myung Choi
    • 1
  • Si Wouk Kim
    • 2
  • Sung Haeng Lee
    • 1
  1. 1.Department of Cellular and Molecular MedicineChosun University School of MedicineGwangjuRepublic of Korea
  2. 2.Department of Environmental EngineeringChosun UniversityGwangjuRepublic of Korea

Personalised recommendations