Structural and mechanistic studies on D-Amino acid oxidase-substrate complex: Implications of the crystal structure of enzyme-substrate analog complex

Journal of Biochemistry

Volumn 122, Issue 4, 1997, Pages 825-833

  Miura, Retsu ^a   Setoyama, Chiaki ^a   Nishina, Yasuzo ^a   Shiga, Kiyoshi ^a   Mizutani, Hisashi ^b   Miyahara, Ikuko ^b   Hirotsu, Ken ^b  

^a KUMAMOTO UNIVERSITY   (Japan)

^b Osaka Prefecture University   (Japan)

Author keywords

D amino acid oxidase; Enzyme substrate complex; Flavoenzyme; Molecular mechanics; Tertiary structure

Indexed keywords

ANTHRANILIC ACID; DEXTRO AMINO ACID OXIDASE; QUERCETIN;

ARTICLE; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PROTON TRANSPORT;

ESCHERICHIA COLI;

EID: 0030667077     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a021829     Document Type: Article

References (41)

1. Krebs, H.A. (1935) Metabolism of amino-acids. III. Deamination of amino acids. Biochem. J. 29, 1620-164 4
2. Krebs, H.A. (1951) Oxidation of D-amino acids in The Enzymes (Sumner, J.B. and Myrbäck, K., eds.) Vol. 2, part 1, pp. 499-535, Academic Press, New York
3. Curti, B., Ronchi, S., and Simonetta, M.P. (1992) D-and L-amino acid oxidases in Chemistry and Biochemistry of Flavoenzymes (Müller, F., ed.) Vol. III, pp. 69-94, CRC Press, Boca Raton, Ann Arbor, London
4. Walsh, C.T., Schonbrunn, A., and Abeles, R.H. (1971) Studies on the mechanism of action of D-amino acid oxidase. Evidence for removal of substrate α-hydrogen as a proton. J. Biol. Chem. 246, 6855-6866
5. Massey, V. and Ghisla, S. (1983) The mechanism of action of flavoprotein-catalyzed reactions in Colloquium-Mosbach, Biological Oxidations (Sund, H. and Ulrich, V., eds.) pp. 114-139, Springer-Verlag, Berlin/Heidelberg
6. Miura, R., Yamano, T., and Miyake, Y. (1985) The reaction mechanism of D-amino acid oxidase with special reference to studies with substrate analogs (in Japanese). Seikagaku 57, 103-116
7. Miura, R. and Miyake, Y. (1988) The reaction mechanism of D-amino acid oxidase: concerted or not concerted? Bioorg. Chem. 16, 97-110
8. Nishina, Y., Sato, K., Miura, R., and Shiga, K. (1995) Structures of charge-transfer complexes of flavoenzyme D-amino acid oxidase: a study by resonance Raman spectroscopy and extended Hückel molecular orbital method. J. Biochem. 118, 614-620
9. Setoyama, C., Miura, R., Nishina, Y., Shiga, K., Mizutani, H., Miyahara, L, and Hirotsu, K. (1996) Crystallization of expressed porcine kidney D-amino acid oxidase and preliminary X-ray crystallographic characterization. J. Biochem. 119, 1114-1117
10. Mizutani, H., Miyahara, I., Hirotsu, K., Nishina, Y., Shiga, K., Setoyama, C., and Miura, R. (1996) Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 Å resolution. J. Biochem. 120, 14-17
11. 2. Proc. Natl. Acad. Sci. USA 93, 7496-7506
12. Massey, V. and Ganther, H. (1965) On the interpretation of the absorption spectra of flavoproteins with special reference to D-amino acid oxidase. Biochemistry 4, 1161-1173
13. Nishina, Y., Shiga, K., Tojo, H., Miura, R., Watari, H., and Yamano, T. (1981) Resonance Raman study of D-amino acid oxidase-inhibitor complexes. J. Biochem. 90, 1515-1520
14. Sakabe, N., Ikemizu, S., Sakabe, K., Higashi, T., Nakagawa, A., Watanabe, N., Adachi, S., and Sasaki, K. (1995) Weissenberg camera for macromolecules with imaging plate data collection system at the Photon Factory: Present status and future plan (invited). Rev. Sci. Instrum. 66, 1276-1281
15. Otwinowski, Z. (1993) Data collection and processing in Proceedings of the CCP4 Study Weekend, pp. 56-62, SERC Daresbury Laboratory, Warrington
16. Brünger, A.T., Kuriyan, J., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics. Science 235, 458-460
17. Jones, T.A., Zou, J.-Y., Vowan, S.W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110-119
18. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
19. Luzzati, V. (1952) Traitement statistique des erreurs dans la détérmination des structures cristallines. Acta Crystallogr. 5, 802-810
20. Nishimoto, K., Imamura, A., Yanaguchi, K., Yamabe, S., and Kitaura, K. (1989) Bunshisekkei no tameno Ryoushikagaku (in Japanese), Kodansha Scientific, Tokyo
21. Hall, L.H., Orchard, B.J., and Tripathy, S.K. (1987) The structure and properties of flavins: molecular orbital study based on totally optimized geometries. I. Molecular geometry investigations. Int. J. Quant. Chem. 31, 195-216
22. Dixon, M. and Kleppe, K. (1965) D-Amino acid oxidase. II. Specificity, competitive inhibition and reaction sequence. Biochim. Biophys. Acta 96, 368-382
23. Miyake, Y., Abe, T., and Yamamo, T. (1972) On the reaction of D-amino acid oxidase with β-chloroalanine. Z. Naturforsch. 27b, 1376-1378
24. Miyake, Y., Abe, T., and Yamano, T. (1973) On the reaction of D-amino acid oxidase with β-chloro-D-alanine. J. Biochem. 73, 1-11
25. Walsh, C.T., Schonbrunn, A., and Abeles, R.H. (1971) Studies on the mechanism of action of D-amino acid oxidase. Evidence for removal of substrate α-hydrogen as a proton. J. Biol. Chem. 246, 6855-6866
26. Walsh, C.T., Krode, E., Massey, V., and Abeles, R.H. (1973) Studies on the elimination reaction of D-amino acid oxidase with α-amino-β-chlorobutyrate. Further evidence for abstraction of substrate α-hydrogen as a proton. J. Biol. Chem. 248, 1946-1955
27. Cheung, Y.-F. and Walsh, C. (1976) Stereochemical analysis of the elimination reaction catalyzed by D-amino acid oxidase. Biochemistry 15, 2432-2441
28. Dang, T.-Y., Cheung, Y.-F., and Walsh, C. (1976) Reactions of β-fluoroalanine and β-bromoalanine with D-amino acid oxidase. Biochem. Biophys. Res. Commun. 72, 960-968
29. Hersh, L.B. and Jorns, M.S. (1975) Use of 5-deaza FAD to study hydrogen transfer in the D-amino acid oxidase reaction. J. Biol. Chem. 250, 8728-8734
30. Nishina, Y., Miura, R., Tojo, H., Miyake, Y., Watari, H., and Shiga, K. (1986) A resonance Raman study on the structures of complexes of flavoprotein D-amino acid oxidase. J. Bichem. 99, 329-337
31. Nishina, Y., Shiga, K., Miura, R., Tojo, H., Ohta, M., Miyake, Y., Yamamo, T., and Watari, H. (1983) On the structures of flavoprotein D-amino acid oxidase purple intermediates. A resonance Raman study. J. Biochem. 94, 1979-1990
32. Nishina, Y., Tojo, H., Miura, R., Miyake, Y., and Shiga, K. (1988) Complex formation between anionic semiquinoid form of a flavoenzyme D-amino acid oxidase and ligands. Stabilizing mechanism of anionic semiquinoid flavoeyzyme. J. Biochem. 104, 727-733
33. Fonda, M.L. and Anderson, B.M. (1968) D-Amino acid oxidase. II. Studies of substrate-competitive inhibitors. J. Biol. Chem. 243, 1931-1936
34. Nishina, Y., Sato, K., and Shiga, K. (1990) Proton release from flavoprotein D-amino acid oxidase on complexation with the zwitterionic ligand, trigonelline. J. Biochem. 107, 726-731
35. 13C-enriched flavin adenine dinucleotide. J. Biochem. 102, 1345-1354
36. Fujimori, K. (1995) Kousohannou ni okeru denshi idou to proton idou (in Japanese). Yuki Hannou no Shintenkai (Okuyama, T., Tomoda, S., and Yamataka, H., eds.) pp. 217-226, Tokyo Kagaku Dojin, Tokyo
37. Müller, F. (1991) Free flavin: synthesis, chemical and physical properties in Chemistry and Biochemistry of Flavoenzymes (Müller, F., ed.) Vol. I, pp. 1-71, CRC Press, Boca Raton, Ann Arbor, London
38. Nishina, Y., Tojo, H., and Shiga, K. (1988) Resonance Raman spectra of anionic semiquinoid form of a flavoenzyme, D-amino acid oxidase. J. Biochem. 104, 227-231
39. Yagi, K., Takai, A., and Ohishi, N. (1972) Conversion of the red semiquinone of D-amino acid oxidase to the blue semiquinone by complex formation. Biochim. Biophys. Acta 289, 37-43
40. Pollegioni, L., Blodig, W., and Ghisla, S. (1997) On the mechanism of D-amino acid oxidase. Structure/linear free energy correlations and deuterium kinetic isotope effects using substituted phenylglycines. J. Biol. Chem. 272, 4924-4934
41. Ghisla, S. and Massey, V. (1991) L-Lactate oxidase in Chemistry and Biochemistry of Flavoenzymes (Müller, F., ed.) Vol. II, pp. 243-289, CRC Press, Boca Raton, Ann Arbor, London