Crystal structure of human D-amino acid oxidase: Context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring

Protein Science

Volumn 15, Issue 12, 2006, Pages 2708-2717

  Kawazoe, Tomoya ^a   Tsuge, Hideaki ^a,b   Pilone, Mirella S ^c   Fukui, Kiyoshi ^a  

^a UNIVERSITY OF TOKUSHIMA   (Japan)

^b TOKUSHIMA BUNRI UNIVERSITY   (Japan)

^c UNIVERSITY OF INSUBRIA   (Italy)

Author keywords

Conformational variability; D amino acid oxidase; Homo sapiens; Structurally ambivalent peptides; X ray crystallography

Indexed keywords

BENZOIC ACID; DEXTRO AMINO ACID OXIDASE; FLAVINE ADENINE NUCLEOTIDE; HOLOENZYME; QUERCETIN; RECOMBINANT ENZYME;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ELECTRICITY; ENZYME CONFORMATION; ENZYME PURIFICATION; ENZYME STRUCTURE; HUMAN; HUMAN TISSUE; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AMINO ACIDS, AROMATIC; ANIMALS; BENZOATES; CRYSTALLOGRAPHY; D-AMINO-ACID OXIDASE; FLAVIN-ADENINE DINUCLEOTIDE; FLAVOPROTEINS; HUMANS; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SWINE; YEASTS;

HOMO SAPIENS; SUIDAE;

EID: 33751519528     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062421606     Document Type: Article

References (34)

1. Brandish, P.E., Chiu, C.S., Schneeweis, J., Brandon, N.J., Leech, C.L., Kornienko, O., Scolnick, E.M., Strulovici, B., and Zheng, W.J. 2006. A cell-based ultra-high-throughput screening assay for identifying inhibitors of D-amino acid oxidase. J. Biomol. Screen. 11: 481-487.
2. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
3. Chumakov, I., Blumenfeld, M., Guerassimenko, O., Cavarec, L., Palicio, M., Abderrahim, H., Bougueleret, L., Barry, C., Tanaka, H., La Rosa, P., et al. 2002. Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia. Proc. Natl. Acad. Sci. 99: 13675-13680.
4. Collaborative Computational Project, Number 4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
5. Fukui, K. and Miyake, Y. 1992. Molecular cloning and chromosomal localization of a human gene encoding D-amino-acid oxidase. J. Biol. Chem. 267: 18631-18638.
6. Fukui, K., Watanabe, F., Shibata, T., and Miyake, Y. 1987. Molecular cloning and sequence analysis of cDNAs encoding pig kidney D-amino acid oxidase. Biochemistry 26: 3612-3618.
7. Fukui, K., Momoi, K., Watanabe, F., and Miyake, Y. 1988. In vivo and in vitro expression of pig D-amino acid oxidase: In vitro system for the synthesis of a functional enzyme. Biochemistry 27: 6693-6697.
8. Gouet, P., Robert, X., and Courcelle, E. 2003. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31: 3320-3323.
9. Holm, L. and Sander, C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233: 123-138.
10. Krebs, H.A. 1935. Metabolism of amino-acids. III. Deamination of amino-acids. Biochem. J. 29: 1620-1644.
11. Kuznetsov, I.B. and Rackovsky, S. 2003. On the properties and sequence context of structurally ambivalent fragments in proteins. Protein Sci. 12: 2420-2433.
12. Mattevi, A., Vanoni, M.A., Todone, F., Rizzi, M., Teplyakov, A., Coda, A., Bolognesi, M., and Curti, B. 1996. Crystal structure of D-amino acid oxidase: A case of active site mirror-image convergent evolution with flavocytochrome b2. Proc. Natl. Acad. Sci. 93: 7496-7501.
13. Michalopoulos, I., Torrance, G.M., Gilbert, D.R., and Westhead, D.R. 2004. TOPS: An enhanced database of protein structural topology. Nucleic Acids Res. 32: D251-D254.
14. Miura, R., Setoyama, C., Nishina, Y., Shiga, K., Mizutani, H., Miyahara, I., and Hirotsu, K. 1997. Structural and mechanistic studies on D-amino acid oxidase·substrate complex: Implications of the crystal structure of enzyme·substrate analog complex. J. Biochem. 122: 825-833.
15. Miyano, M., Fukui, K., Watanabe, F., Takahashi, S., Tada, M., Kanashiro, M., and Miyake, Y. 1991. Studies on Phe-228 and Leu-307 recombinant mutants of pig kidney D-amino acid oxidase: Expression, purification, and characterization. J. Biochem. 109: 171-177.
16. Mizutani, H., Miyahara, I., Hirotsu, K., Nishina, Y., Shiga, K., Setoyama, C., and Miura, R. 1996. Three-dimensional structure of pig kidney D-amino acid oxidase at 3.0 Å resolution. J. Biochem. 120: 14-17.
17. Mizutani, H., Miyahara, I., Hirotsu, K., Nishina, Y., Shiga, K., Setoyama, C., and Miura, R. 2000. Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin. J. Biochem. 128: 73-81.
18. Molla, G., Sacchi, S., Bernasconi, M., Pilone, M.S., Fukui, K., and Pollegioni, L. 2006. Characterization of human D-amino acid oxidase. FEBS Lett. 580: 2358-2364.
19. Momoi, K., Fukui, K., Watanabe, F., and Miyake, Y. 1988. Molecular cloning and sequence analysis of cDNA encoding human kidney D-amino acid oxidase. FEBS Lett. 238: 180-184.
20. 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.
21. Nicholls, A., Sharp, K.A., and Honig, B. 1991. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11: 281-296.
22. Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
23. Park, H.K., Shishido, Y., Ichise-Shishido, S., Kawazoe, T., Ono, K., Iwana, S., Tomita, Y., Yorita, K., Sakai, T., and Fukui, K. 2006. Potential role for astroglial D-amino acid oxidase in extracellular D-serine metabolism and cytotoxicity. J. Biochem. 139: 295-304.
24. Pilone, M.S. 2000. D-Amino acid oxidase: New findings. Cell. Mol. Life Sci. 57: 1732-1747.
25. Pollegioni, L., Fukui, K., and Massey, V. 1994. Studies on the kinetic mechanism of pig kidney D-amino acid oxidase by site-directed mutagenesis of tyrosine 224 and tyrosine 228. J. Biol. Chem. 269: 31666-31673.
26. Pollegioni, L., Diederichs, K., Molla, G., Umhau, S., Welte, W., Ghisla, S., and Pilone, M.S. 2002. Yeast D-amino acid oxidase: Structural basis of its catalytic properties. J. Mol. Biol. 324: 535-546.
27. Raibekas, A.A., Fukui, K., and Massey, V. 2000. Design and properties of human D-amino acid oxidase with covalently attached flavin. Proc. Natl. Acad. Sci. 97: 3089-3093.
28. Sawa, A. and Snyder, S.H. 2002. Schizophrenia: Diverse approaches to a complex disease. Science 296: 692-695.
29. Setoyama, C., Miura, R., Nishina, Y., Shiga, K., Mizutani, H., Miyahara, I., and Hirotsu, K. 1996. Crystallization of expressed pig kidney D-amino acid oxidase and preliminary X-ray crystallographic characterization. J. Biochem. 119: 1114-1117.
30. Setoyama, C., Nishina, Y., Tamaoki, H., Mizutani, H., Miyahara, I., Hirotsu, K., Shiga, K., and Miura, R. 2002. Effects of hydrogen bonds in association with flavin and substrate in flavoenzyme D-amino acid oxidase. The catalytic and structural roles of Gly313 and Thr317. J. Biochem. 131: 59-69.
31. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
32. Todone, F., Vanoni, M.A., Mozzarelli, A., Bolognesi, M., Coda, A., Curti, B., and Mattevi, A. 1997. Active site plasticity in D-amino acid oxidase: A crystallographic analysis. Biochemistry 36: 5853-5860.
33. Umhau, S., Pollegioni, L., Molla, G., Diederichs, K., Welte, W., Pilone, M.S., and Ghisla, S. 2000. The X-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation. Proc. Natl. Acad. Sci. 97: 12463-12468.
34. Yagi, K., Nagatsu, T., and Ozawa, T. 1956. Inhibitory action of chlorpromazine on the oxidation of D-amino-acid in the diencephalon part of the brain. Nature 177: 891-892.