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Crystal structure of NADH oxidase from Thermus thermophilus

Nature Structural Biology volume 2, pages 1109–1114 (1995)Cite this article

Abstract

The crystal structures of the flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) containing isoforms of NADH oxidase from Thermus thermophilus have been determined by isomorphous and molecular replacement and refined to 2.3 Å and 1.6 Å resolution with R-values of 18.5 % and 18.6 % respectively. The structure of the homodimeric enzyme consists of a central 4-stranded antiparallel β-sheet covered by helices, a more flexible domain formed by two helices, and a C-terminal excursion connecting the subunits. The active sites are located in a deep cleft between the subunits. The binding site of the flavin cofactor lacks the common nucleotide binding fold and is different from the FMN binding site found in flavodoxins.

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References

  1. Park, H.-J. et al. Purification and characterization of a NADH oxidase from the thermophilic Thermus thermophilus . Eur. J. Biochem. 205, 881–885 (1992)

    Article  CAS  Google Scholar 

  2. Malstrm, B.G. Enzymology of oxygen. A. Rev. Biochem. 51, 21–59 (1982).

    Article  Google Scholar 

  3. Park, H.-J., Reiser, C.O.A., Kreutzer, R. & Sprinzl, M. Molecular cloning and nucleotide sequence of the gene encoding a H2O2-forming NADH oxidase from the thermophilic Thermus thermophilus HB8 and its expression in Escherichia coli . Eur. J. Biochem. 205, 875–879 (1992).

    Article  CAS  Google Scholar 

  4. Erdmann, H., Hecht, H.-J. & Schmid, R.D. preparation, properties and crystallization of a recombinant NADH oxidase. Dechema Biotechnology Conferences 5, 93–95 (1992).

    CAS  Google Scholar 

  5. Erdmann, H. et al. Crystallization and preliminary X-ray diffraction studies of a NADH oxidase from Thermus thermophilus HB8. J. molec. Biol. 230, 1086–1088 (1993).

    Article  CAS  Google Scholar 

  6. Dolin, M.I. The oxidation and peroxidation of DPNH2 in extracts of Streptococcus faecalis 10C1. Arch, biochem. Biophys. 46, 483–485. (1953).

    Article  CAS  Google Scholar 

  7. Thomas, E.L. & Pera, K.A. Oxygen metabolism of Streptococcus mutans: Uptake of oxygen and release of superoxide and hydrogen peroxide. J. Bacteriol. 154, 1236–1244 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Koike, K., Koboyashi, T., Ito, S. & Saitoh, M. Purification and characterization of NADH oxidase from a strain of Leuconostoc mesenteroides . J. Biochem. 97, 1279–1288. (1985).

    Article  CAS  Google Scholar 

  9. Schmidt, H.L., Stöcklein, W., Danzer, J., Kirch, P. & Limbach, B. Isolation and properties of an H2O-forming NADH oxidase from Streptococcus faecalis. Eur. J. Biochem. 15, 149–155 (1986).

    Article  Google Scholar 

  10. Ahmed, S.A. & Claiborne, A. The streptococcal flavoprotein NADH oxidase. J. biol. Chem. 264, 19856–19863 (1989).

    CAS  PubMed  Google Scholar 

  11. Liu, X.L. & Scopes, R.K., Cloning, sequencing and expression of the gene encoding NADH oxidase from the extreme anaerobic thermophile Thermoanaerobium brockii . Biochim. biophys. Acta, 1174, 184–190 (1993).

    Google Scholar 

  12. Anders, R.F., Hogg, D.M. & Jago, G.R. Formation of hydrogen peroxide by group n streptococci and its effect on their growth and metabolism. App. Microbiol. 19, 602–612 (1970).

    Google Scholar 

  13. Gtz, F., Sedewitz, B. & Elstner, E.F. Oxygen utilization by Lactobacillus plantarum: 1. Oxygen consuption reactions. Arch. Microbiol. 125, 209–214 (1980).

    Article  Google Scholar 

  14. Saeki, Y., Nozaki, M. & Matsumoto, K. Purification and properties of NADH oxidase from Bacillus megaterium . J. Biochem. 98, 1433–1440 (1985).

    Article  CAS  Google Scholar 

  15. Cocco, D., Rinaldi, A., Savini, I., Cooper, J.M. & Bannister, J.V. NADH oxidase from the extreme thermophile Thermus aquaticus YT-1: Purification and characterization. Eur. J. Biochem. 174, 267–271 (1988).

    Article  CAS  Google Scholar 

  16. Inouye, S. NAD(P)H-flavin oxidoreductase from the bioluminescent bacterium, Vibrio fischeri ATCC 7744, is a flavoprotein. FEBS Letts. 347, 163–168 (1994).

    Article  CAS  Google Scholar 

  17. Zenno, S., Saigo, K., Kanoh, H. & Inouye, S. Identification of the gene encoding the major NAD(P)H-flavin oxidoreductase of the bioluminescent bacterium Vibrio fisheri ATCCA 7744. J. Bacteriol. 176 (12) 3536–3543 (1994).

    Article  CAS  Google Scholar 

  18. Chenault, H.K. & Whitesides, G.M. Lactate dehydrogenase-catalyzed regeneration of NAD from NADH for use in enzyme-catalyzed synthesis. Bioorganic. Chem. 17, 400–409 (1989).

    Article  CAS  Google Scholar 

  19. McNeil, C.J., Spoors, J.A., Cocco, D.; Cooper, J.M. & Bannister, J.V. Thermostable reduced nicotinamide adenine dinucleotide oxidase: Application to amperometric enzyme assay. Anal. Chem. 61, 25–29 (1989).

    Article  CAS  Google Scholar 

  20. Somasundrum, M., Hall, J. & Bannister, J.V. Amperimetric NADH determination via both directet and mediated electron transfer by NADH oxidase from Thermus aquaticus YT.1. Analytica Chimica Acta 295, 47–57 (1994).

    Article  CAS  Google Scholar 

  21. Tabata, M., Koushima, F. & Totani, M. Use of a biosensor consisting of an immobilized NADH oxidase column and a hydrogen peroxide electrode for the determination of serum lactate dehydrogenase activity. Analytica Chimica Acta 298, 113–119k (1994).

    Article  CAS  Google Scholar 

  22. Hecht, H.J., Kalisz, H.M., Hendle, J., Schmid, R.D. & Schomburg, D. Crystal structure of Glucose oxidase from Aspergillus niger refined at 2.3 resolution. J. molec. Biol. 229, 153–172 (1993).

    Article  CAS  Google Scholar 

  23. Vrielink, A., Lloyd, L.F. & Blow, D.M. Crystal structure of cholesterol oxidase from Brevibacterium sterolicum refined at 1.8 Å resolution. J. molec. Biol. 219, 233–254 (1991).

    Article  Google Scholar 

  24. Fukuyama, K., Matsubara, H. & Rogers, L.J. Crystal structure of oxidized flavodoxin from a red alga Chondrus crispus refined at 1.8 Å resolution. J. molec. Biol. 225, 775–789 (1992).

    Article  CAS  Google Scholar 

  25. Pai, E.F., Karplus, P.A. & Schulz, G.E. Crystallographic analysis of the binding of NADPH, NADPH fragments, and NADPH analogues to gluthatione reductase. Biochemistry 27, 4465–4474 (1988).

    Article  CAS  Google Scholar 

  26. Zenno, S., Saigo, K., Kanoh, H. & Inouye, S. Identification of the gene encoding the major NAD(P)H-flavin oxidoreductase of the bioluminescent bacterium Vibrio fischeri ATCC 7744. J. Bact. 176, 3536–3543 (1994).

    Article  CAS  Google Scholar 

  27. Inouye, S. NAD(P)H-flavin oxidoreductase from the bioluminescent bacterium, Vibrio fischeri ATCC 7744, is a flavoprotein. FEBS Let. 347, 163–168 (1994).

    Article  CAS  Google Scholar 

  28. Matthews, B.W. Solvent content of protein crystals. J. molec. Biol. 33, 491–497 (1968).

    Article  CAS  Google Scholar 

  29. CCP4, 1979, The SERC (UK) Collaborative Computing Project No. 4, a Suite of Programs for Protein Crystallography, distributed from Daresbury Laboratory, Warrington WA4 4AD, UK (version 2.1).

  30. Howard, A.J. et al. The use of an imaging proportional counter in macromolecular crystallography. J. appl. Crystallogr. 20, 383–387 (1987).

    Article  CAS  Google Scholar 

  31. Cowtan, K.D. & Main, P. Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints. Acta Crystallogr. D49, 148–157 (1993).

    CAS  Google Scholar 

  32. Jones, T.A. A graphics model building and refinement system for macromolecules. J Appl. Crystallogr. 11, 268–272 (1978).

    Article  CAS  Google Scholar 

  33. Brünger, A.T., Kuriyan, J. & Karplus, M. Refinement by simulated annealing. Science 235, 458–460 (1987).

    Article  Google Scholar 

  34. Engh, R.A. & Huber, R. Accurate bond and angle parameters for x-ray protein structure refinement. Acta Crystallogr. A47, 392–400 (1991).

    Article  CAS  Google Scholar 

  35. Bernstein, F.C. et al. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. molec. Biol. 112, 535–542 (1977).

    Article  CAS  Google Scholar 

  36. Brünger, A.T. Extension of molecular replacement: a new strategy based on patterson correlation refinement. Acta Crystallogr. A46, 46–57 (1990).

    Article  Google Scholar 

  37. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110–119 (1991).

    Article  CAS  Google Scholar 

  38. Kraulis, P.J. “MOLSCRIPT”: a program to produce both detailed and schematic plots of protein structures. J. appl. Cryst. 24, 946–950 (1991) modified by D. Peisach (Peisach@hydra.rose.brandeis.edu) for rendering with Rayshade (rayshade-requests@cs.princeton.edu).

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Molecular Structure Research, GBF(Gesellschaft fr Biotechnologische Forschung), Mascheroder Weg 1, D-38124, Braunschweig, Germany

    H.J. Hecht

  2. Department of Enzyme Technology, GBF(Gesellschaft fr Biotechnologische Forschung), Mascheroder Weg 1, D-38124, Braunschweig, Germany

    H. Erdmann & R.D. Schmid

  3. Laboratorium fr Biochemie, Univ. Bayreuth, D-95440, Bayreuth, Germany

    H.J. Park & M. Sprinzl

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  4. M. Sprinzl
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  5. R.D. Schmid
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Hecht, H., Erdmann, H., Park, H. et al. Crystal structure of NADH oxidase from Thermus thermophilus. Nat Struct Mol Biol 2, 1109–1114 (1995). https://doi.org/10.1038/nsb1295-1109

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