The Structure of a Bacterial l-Amino Acid Oxidase from Rhodococcus opacus Gives New Evidence for the Hydride Mechanism for Dehydrogenation

Journal of Molecular Biology

Volumn 367, Issue 1, 2007, Pages 234-248

  Faust, Annette ^a   Niefind, Karsten ^a   Hummel, Werner ^b   Schomburg, Dietmar ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

enzyme mechanism; FAD containing; flavoenzyme; GR2 family; l amino acid oxidase

Indexed keywords

AMINO ACID; AMINO ACID OXIDASE; BACTERIAL ENZYME; DEXTRO AMINO ACID OXIDASE; FLAVINE ADENINE NUCLEOTIDE; FLAVOPROTEIN; OXIDOREDUCTASE; PROTON; SNAKE VENOM; TERNARY COMPLEX FACTOR;

ARTICLE; DEHYDROGENATION; ENANTIOSELECTIVITY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME MECHANISM; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ENZYME SUBUNIT; KIDNEY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTON TRANSPORT; RHODOCOCCUS; RHODOCOCCUS OPACUS; SWINE; YEAST;

BACTERIA (MICROORGANISMS); RHODOCOCCUS OPACUS; SUIDAE;

EID: 33847013408     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.11.071     Document Type: Article

References (61)

1. 2. Proc. Natl Acad. Sci. USA 93 (1996) 7496-7501
2. Mizutani H., Miyahara I., Hirotsu K., Nishina Y., Shiga K., Setoyama C., and Miura R. 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. (Tokyo) 128 (2000) 73-81
3. Pawelek P.D., Cheah J., Coulombe R., Macheroux P., Ghisla S., and Vrielink A. The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site. EMBO J. 19 (2000) 4204-4215
4. Miura R., Setoyama C., Nishina Y., Shiga N., Mizutani H., Miyahara I., and Hirotsu K. Structural and mechanical studies on D-amino acid oxidase x substrate complex: inplications of the crystal structure of enzyme x analog complex. J. Biochem. (Tokyo) 122 (1997) 825-833
5. Pollegioni L., Diederichs K., Molla G., Umhau S., Welte W., Ghisla S., and Pilone M.S. Yeast D-amino acid oxidase: structural basis of its catalytic properties. J. Mol. Biol. 324 (2002) 535-546
6. Umhau S., Pollegione L., Molla G., Diederichs K., Welte W., Pilone M.S., and Ghisla S. 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. USA 97 (2000) 12463-12468
7. Mizutani H., Miyahara I., Hirotsu K., Nishina Y., Shiga K., Setoyama C., and Miura R. Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 Å resolution. J. Biochem. (Tokyo) 120 (1996) 14-17
8. Boehmer A., Mueller A., Passarge M., Liebs P., Honeck H., and Mueller H.G. A novel L-glutamate oxidase from Streptomyces endus. Eur. J. Biochem. 182 (1989) 327-332
9. Kamei T., Asano K., Suzuki H., Matsukaki M., and Nakamura S. L-Glutamate oxidase from Streptomyces violascens. I. Production, isolation and some properties. Chem. Pharm. Bull. 31 (1983) 1307-1314
10. Kamei T., Asano K., Kondo H., Matsukaki M., and Nakamura S. L-Glutamate oxidase from Streptomyces violascens II Properties. Chem. Pharm. Bull. 31 (1983) 3609-3616
11. Koyama H. Further characterization of a novel L-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. J. Biochem. (Tokyo) 93 (1983) 1313-1319
12. Cioaca C., and Ivanof A. Bacterial amino acid oxidases. I. L-amino acid oxidase and its distribution in bacteria. Arch. Roum. Pathol. Exp. Microbiol. 33 (1974) 211-222
13. Massad G., Zhao H., and Mobley H.L. Proteus mirabilis amino acid deaminase: cloning, nucleotide sequence, and characterization of aad. J. Bacteriol. 177 (1995) 5878-5883
14. Nishizawa T., Aldrich C.C., and Sherman D.H. Molecular analysis of the rebeccamin L-amino acid oxidase from Lechevalieria aerocolonigenes ATCC 39243. J. Bacteriol. 187 (2005) 2084-2092
15. Zeller A. Über eine neue l-aminosäure-oxydase. Helv. Chim. Acta 27 (1944) 1888-1903
16. Sanchez E., and Magalhaes A. Purification and partial characterization of an L-amino acid oxidase from bustmaster snake (Surucucu Pico de Jaca) Lachesis muta muta venom. Braz. J. Med. Biol. Res. 24 (1991) 249-260
17. Tan N., and Saifuddin N. Substrate specificity of king cobra (Ophiophagus Hannah) venom L-amino acid oxidase. Int. J. Biochem. 23 (1991) 323-327
18. Tan N., and Swaminathan S. Purification properties of the L-amino acid oxidase from monocellate cobra (Naja Naja Kaouthia) venom. Int. J. Biochem. 24 (1992) 967-973
19. Ponnudurai G., Chung M.C., and Tan N.H. Purification and properties of the L-amino acid oxidase from Malayan pit viper (Calloselasma rhodostoma) venom. Arch. Biochem. Biophys. 313 (1994) 373-378
20. Torii S., Naito M., and Tsuruo T. Apoxin I, a novel apoptosis-inducing factor with L-amino acid oxidase activity purified from Western diamond rattlesnake venom. J. Biol. Chem. 272 (1994) 9539-9542
21. Souza D.H.F., Eugenio L.M., Fletcher J.E., Jiang M., Garratt R.C., Oliva G., and Selistre-de-Araujo H.S. Isolation and structural characterization of a cytotoxic L-amino acid oxidase from Agkistrodon contortrix laticinctus snake venom: preliminary crystallographic data. Arch. Biochem. Biophys. 368 (1999) 285-290
22. Ahn M.Y., Ryu K.S., Lee Y.W., and Kim Y.S. Cytotoxicity of L-amino acid oxidase activity of crude insect drugs. Arch. Pharm. Res. 23 (2000) 477-481
23. Le K.H., and Villanueva V.R. Purification and characterization of epsilon-N-trimethyllysin L-amino oxidase from Neurospora crassa. Biochim. Biophys. Acta 524 (1978) 288-296
24. Kusakabe H., Kodama K., Kuninaka A., Yoshino H., Misono H., and Soda K. A new antitumor enzyme, L-lysine alpha-oxidase from Trichoderma viride. Purification and enzymological properties. J. Biol. Chem. 255 (1980) 976-981
25. Piedras P., Pineda M., Munoz J., and Cardenas J. Purification and characterization of an L-amino acid oxidase from Chlamydomonas reinhardtii. Planta 188 (1992) 13-18
26. Coudert M. Characterization and physiological functions of a soluble L-amino acid oxidase in Corynebacterium. Arch. Microbiol. 102 (1975) 151-153
27. Braun M., Kim J.M., and Schmid R.D. Purification and some properties of an extracellular L-amino acid oxidase from Cellulomonas cellulans AM8 isolated from soil. Appl. Microbiol. Biotechnol. 37 (1992) 594-598
28. Brearley G.M., Price C.P., Atkinson T., and Hammond P.M. Purification and partial characterization of a broad-range L-amino acid oxidase from Bacillus carotarum 2Pfa isolated from soil. Appl. Microbiol. Biotechnol. 41 (1994) 670-676
29. DeBusk R.M., and Ogilvie S. Participation of an extracellular deaminase in amino acid utilization by Neurospora crassa. J. Bacteriol. 159 (1984) 583-589
30. Munoz-Blanco J., Hidalgo-Martinez J., and Cardenas J. Extracellular deamination of L-amino acids by Chlamydomonas reinhadtii cells. Planta 182 (1990) 194-198
31. Varadi M., Adanyi N., Szabo E.E., and Trummer N. Determination of the ration of D- and L-amino acids in brewing by an immobilised amino acid oxidase enzyme reactor coupled to amperometric detection. Biosens. Bioelectron. 14 (1999) 335-340
32. Sarkar P., Tothill I.E., Setford S.J., and Turner A.P.F. Screen-printed amperometric biosensors for the rapid measurement of L- and D-amino acids. The Analyst 124 (1999) 865-870
33. Liu L., and Wang J. Remarkable thermostability of bioelectrodes based on enzymes immobilized within hydrophobic semi-solid matrices. Biotechnol. Appl. Biochem. 30 (1999) 177-183
34. Takahashi E., Furui M., Seko H., and Shibatani T. D-methionine preparation from racemic methionines by Proteus vulgaris IAM 12003 with asymmetric degrading activity. Appl. Microbiol. Biotechnol. 47 (1997) 173-179
35. Hanson R.L., Bembenek K.S., Patel R.N., and Szarka L.J. Transformation of N-epsilon-CBZ-L-lysine to CBT-L-oxylysine using L-amino acid oxidase from Providencia alcalifaciens and L-2-hydroxy-isocaproate dehydrogenase from Lactobacillus confusus. Appl. Microbiol. Biotechnol. 37 (1992) 599-603
36. Geueke B., and Hummel W. A new bacterial L-amino acid oxidase with a broad substrate specificity: purification and characterization. Enyzme Microbiol. Technology 31 (2002) 77-87
37. Zhang H., Teng M., Niu L., Wang Y., Wang Y., Huang Q., Hao Q., et al. Purification, partial characterization, crystallization and structural determination of AHP-LAAO, a novel L-amino acid oxidase with cell apoptosis-inducing activity from Agkistrodon halys pallas venom. Acta Crystallog. sect. D 60 (2004) 974-977
38. Schomburg D., and Reichelt J. A comprehensive protein modeling program system. J. Mol. Graph. 6 (1998) 161-165
39. Dym O., and Eisenberg D. Sequence-structure analysis of FAD-containing proteins. Protein Scie. 10 (2001) 1712-1728
40. Vallon O. sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure. Proteins: Struct. Funct. Genets. 38 (2000) 95-114
41. Wierenga R.K., Drenth J., and Schultz G.E. Comparison of the three-dimensional protein and nucleotide structure of the FAD-binding domain of p-hydroxybenzoate hydroxylase with the FAD- as well as NADPH-binding domains of gluthation reductase. J. Mol. Biol. 167 (1983) 725-739
42. Porter D.J.T., and Bright H.J. Location of hydrogen transfer steps in the mechanism of reduction of L-amino acid oxidase. Biochem. Biophys. Res. Commun. 36 (1969) 209-214
43. Geyer A., Fitzpatrick T.B., Pawelek P.D., Kitzing K., Vrielink A., Ghisla S., and Macheroux P. Structure and characterization of the glycan moiety of L-amino-acid oxidase from the Malayan pit viper Calloselasma rhodostoma. Eur. J. Biochem. 268 (2001) 4044-4053
44. Binda C., Coda A., Angelini R., Federico R., Ascenzi P., and Mattevi A. A 30 Å long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase. Structure 7 (1999) 265-276
45. Zhou B.P., Wu B., Kwan S., and Abell C.W. Characterization of a highly conserved FAD-binding site in human monoamine oxidase B. J. Biol. Chem. 273 (1998) 14862-14868
46. Lederer F. In: Mueller F. (Ed). Chemistry and Biochemistry of Flavoenzymes vol. 2 (1991), CRC, Boca Raton, FL
47. Xia Z.X., Shamala N., Bethge P.H., Lim L.W., Bellamy H.D., Xuong N.H., et al. Three-dimensional structure of the flavocytochrome b2 from baker's yeast at 3.0 Å resolution. Proc. Natl Acad. Sci. USA 84 (1987) 2629-2633
48. Popov A., and Bourenkov G.P. Choice of data-collection parameters based on statistic modeling. Acta Crystallog. sect. D 59 (2003) 1145-1153
49. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: Carter C.W.J., and Sweet R.M. (Eds). Methods in Enzymology vol. 276 (1997), Academic Press, San Diego
50. Wang B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115 (1985) 90-112
51. Bricogne G., Vonrhein C., Flensburg C., Schiltz M., and Paciorek W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP2.0. Acta Crystallog. sect. D 59 (2003) 2023-2030
52. Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6 (1999) 458-463
53. Collaborative Computational Project, No. 4. The CCP4 Suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
54. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for binding protein models in electron density maps and the location of errors in this models. Acta Crystallog. sect. A 47 (1991) 110-119
55. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog. sect D 60 (2004) 2126-2132
56. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., et al. The Protein Data Bank. Nucl. Acids Res. 28 (2000) 235-242
57. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
58. Altschul S., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment tool. J. Mol. Biol. 215 (1990) 403-410
59. Thompson J., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through a sequence weighting, positions-specific gap penalties and weigh matrix choice. Nucl. Acids Res. 22 (1990) 4673-4680
60. Bruenger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., et al. Crystallography and NMR Systems: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
61. Faust A., Geueke B., Niefind K., Hummel W., and Schomburg D. Crystallization and preliminary X-ray analysis of a bacterial L-amino-acid oxidase from Rhodococcus opacus. Acta Crystallog. sect. F 62 (2006) 279-281