High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole. Implications for inhibitor specificity and drug design

Biochimie

Volumn 94, Issue 5, 2012, Pages 1172-1179

  Chen, Zhi Wei ^a   Vignaud, Caroline ^b   Jaafar, Adil ^c   Lévy, Bernard ^c   Guéritte, Franoise ^d   Guénard, Daniel ^d   Lederer, Florence ^c   Mathews, F Scott ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LABORATOIRE D ENZYMOLOGIE ET BIOCHIMIE STRUCTURALES   (France)

^c UNIVERSITÉ PARIS SUD   (France)

^d INSTITUT DE CHIMIE DES SUBSTANCES NATURELLES   (France)

Author keywords

Crystal structure; Flavoprotein; Homology; Hydrogen bond; Inhibitor; Long chain hydroxy acid oxidase

Indexed keywords

(S) 2 HYDROXY ACID OXIDASE; 4 CARBOXY 5 [(4 CHLOROPHENYL)SULFANYL] 1, 2, 3 THIADIAZOLE; HISTIDINE; HYDROXY ACID OXIDASE A; LACTATE DEHYDROGENASE (CYTOCHROME); LONG CHAIN HYDROXY ACID OXIDASE; NITROGEN; OXIDOREDUCTASE INHIBITOR; SULFUR; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG BINDING; DRUG DESIGN; DRUG SPECIFICITY; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME STRUCTURE; HYDROPHOBICITY; NONHUMAN; PROTON TRANSPORT; RAT;

ALCOHOL OXIDOREDUCTASES; ANIMALS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; ENZYME INHIBITORS; FLAVOPROTEINS; HYDROGEN BONDING; MOLECULAR STRUCTURE; PROTEIN STRUCTURE, SECONDARY; RATS; THIADIAZOLES;

RATTUS; SPINACIA OLERACEA;

EID: 84862789275     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2012.02.003     Document Type: Article

References (46)

1. M. Blanchard, D.E. Green, V. Nocito, and S. Ratner l-amino acid oxidase of animal tissue J. Biol. Chem. 155 1944 421 440
2. M. Blanchard, D.E. Green, V. Nocito-Carroll, and S. Ratner l-hydroxy acid oxidase J. Biol. Chem. 163 1946 137 144
3. M. Nakano Comparison of the enzyme oxidizing thyroid hormone with l-amino acid oxidase Biochim. Biophys. Acta 92 1964 472 481
4. J.L. Stevens, P.B. Hatzinger, and P.J. Hayden Quantitation of multiple pathways for the metabolism of nephrotoxic cysteine conjugates using selective inhibitors of l-α-hydroxy acid oxidase (l-amino acid oxidase) and cysteine conjugate ß-lyase Drug Metab. Dispos. 17 1989 297 303
5. J.L. Stevens, J.D. Robbins, and R.A. Byrd A purified cysteine conjugate ß-lyase from rat kidney cytosol. Requirement for an α-keto acid or an amino acid oxidase for activity and identity with soluble glutamine transaminase J. Biol. Chem. 261 1986 15529 15537
6. E.J. Brush, and G.A. Hamilton Thiol-glyoxylate adducts as substrates for rat kidney l-α-hydroxy acid oxidase Biochem. Biophys. Res. Commun. 103 1981 1194 1200
7. 2 catalyzed by l-hydroxy acid oxidase Bioorg. Chem. 13 1985 1 13
8. H. Ozasa, S. Horikawa, and K. Ota Methylguanidine synthase from rat kidney is identical to long-chain l-2-hydroxy acid oxidase Nephron 68 1994 279
9. T. Yokozawa, N. Fujitsuka, H. Oura, T. Akao, K. Kobashi, K. Ienaga, K. Nakamura, and M. Hattori Purification of methylguanidine synthase from the rat kidney Nephron 63 1993 452 457
10. P. De Deyn, B. Marescau, W. Lornoy, I. Becaus, I. Van Leuven, L. Van Gorp, and A. Lowenthal Serum guanidino compound levels and the influence of a single hemodialysis in uremic patients undergoing maintenance hemodialysis Nephron 45 1987 291 295
11. P.P. De Deyn, R. D'Hooge, P.P. Van Bogaert, and B. Marescau Endogenous guanidino compounds as uremic neurotoxins Kidney Int. Suppl. 78 2001 S77 S83
12. K. Nakamura, and K. Ienaga Creatol (5-hydroxycreatinine), a new toxin candidate in uremic patients Experientia 46 1990 470 472
13. T. Yokozawa, N. Fujitsuka, H. Oura, K. Ienaga, and K. Nakamura Comparison of methylguanidine production from creatinine and creatol in vivo Nephron 58 1991 125 126
14. C.J. Danpure Primary hyperoxaluria C.R. Scriver, A.L. Beaudet, W.S. Sly, D. Valle, B. Childs, K.W. Kinzler, B. Vogelstein, The Metabolic and Molecular Bases of Inherited Disease 2001 McGrax-Hill New York 3323 3367
15. R.P. Holmes Pharmacological approaches in the treatment of primary hyperoxaluria J. Nephrol. 11 Suppl. 1 1998 32 35
16. A. Belmouden, K.H.D. Lê, F. Lederer, and H.-J. Garchon Molecular cloning and nucleotide sequence of cDNA encoding rat kidney long-chain l-2-hydroxy acid oxidase. Expression of the catalytically active recombinant protein as a chimaera Eur. J. Biochem. 214 1993 17 25
17. J.M. Jones, J.C. Morrell, and S.J. Gould Identification and characterization of HAOX1, HAOX2, and HAOX3, three human peroxisomal 2-hydroxy acid oxidases J. Biol. Chem. 275 2000 12590 12597
18. J.M. Jones, J.C. Morrell, and S.J. Gould Identification and characterization of HAOX1, HAOX2, and HAOX3, three human peroxisomal 2-hydroxy acid oxidases J. Biol. Chem. 275 2004 35122
19. L.M. Cunane, J.D. Barton, Z.-w. Chen, K.H.D. Lê, D. Amar, F. Lederer, and F.S. Mathews Crystal structure analysis of recombinant rat kidney long-chain α-hydroxy acid oxidase Biochemistry 44 2005 1521 1531
20. Y. Lindqvist Refined structure of spinach glycolate oxidase at 2 resolution J. Mol. Biol. 209 1989 151 166
21. M.S. Murray, R.P. Holmes, and W.T. Lowther Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design Biochemistry 47 2008 2439 2449
22. K. Maeda-Yorita, K. Aki, H. Sagai, H. Misaki, and V. Massey l-lactate oxidase and l-lactate monooxygenase: mechanistic variations on a common structural theme Biochimie 77 1995 631 642
23. Y. Umena, K. Yorita, T. Matsuoka, A. Kita, K. Fukui, and Y. Morimoto The crystal structure of l-lactate oxidase from Aerococcus viridans at 2.1 resolution reveals the mechanism of strict substrate recognition Biochem. Biophys. Res. Commun. 350 2006 249 256
24. N. Sukumar, A.R. Dewanti, B. Mitra, and F.S. Mathews High resolution structures of an oxidized and reduced flavoprotein: the water switch in a soluble form of mandelate dehydrogenase J. Biol. Chem. 279 2004 3749 3757
25. 2 at 2.4 resolution J. Mol. Biol. 212 1990 837 863
26. K. Stenberg, and Y. Lindqvist Three-dimensional structures of glycolate oxidase with bound active-site inhibitors Protein Sci. 6 1997 1009 1015
27. J.M. Bourhis, C. Vignaud, N. Pietrancosta, F. Guéritte, D. Guénard, F. Lederer, and Y. Lindqvist Structure of human glycolate oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole Acta Cryst. Sect. F 65 2009 1246 1253
28. A. Belmouden, and F. Lederer The role of a ß barrel loop 4 extension in modulating the physical and functional properties of long-chain 2-hydroxy acid oxidase isozymes Eur. J. Biochem. 238 1996 790 798
29. C. Vignaud, N. Pietrancosta, E.L. Williams, G. Rumsby, and F. Lederer Purification and characterization of recombinant human liver glycolate oxidase Arch. Biochem. Biophys. 465 2007 410 416
30. 2, expressed independently in Escherichia coli Biochem. J. 309 1995 601 605
31. 2. Inhibition by anion binding in the active site Biochemistry 46 2007 4661 4670
32. M. Dixon The determination of enzyme inhibitor constants Biochem. J. 55 1953 170 171
33. A. Cornish-Bowden A simple graphical method for determining the inhibition constants of mixed, uncompetitive and non-competitive inhibitors Biochem. J. 137 1974 143 144
34. Z. Otwinowski, and W. Minor Processing of x-ray diffraction data collected by oscillation methods Methods Enzymol. 276 1997 307 326
35. The CCP4 suite: programs for protein crystallography Acta Cryst. Sect. D 50 1994 760 763
36. A. Roussel, C. Cambillau, Turbo Frodo, in Silicon Graphics geometry Partners Directory, Silicon Graphic, Mountain View, CA., USA, 1989, pp. 77-78.
37. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, and G.L. Warren Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Cryst. D 54 1998 905 921
38. A.T. Brünger Free R-value: a novel statistical quantity for assessing the accuracy of crystal structures Nature (London) 355 1992 472 475
39. 2 - by product binding to the semiquinone transient: loss of reactivity towards monoelectronic acceptors Eur. J. Biochem. 190 1990 329 342
40. 2 (yeast l-lactate dehydrogenase) Protein Sci. 7 1998 1531 1537
41. 2: comparison with the intact wild-type enzyme Biochemistry 41 2002 4264 4272
42. N. Sukumar, A. Dewanti, A. Merli, G.L. Rossi, B. Mitra, and F.S. Mathews Structures of the G81A mutant form of the active chimera of (S)-mandelate dehydrogenase and its complex with two of its substrates Acta Cryst. Sect. D 65 2009 543 552
43. I. Leiros, E. Wang, T. Rasmussen, E. Oksanen, H. Repo, S.B. Petersen, P. Heikinheimo, and E. Hough The 2.1 structure of Aerococcus viridans l-lactate oxidase (LOX) Acta Cryst. Sect. F 62 2006 1185 1190
44. S.J. Li, Y. Umena, K. Yorita, T. Matsuoka, A. Kita, K. Fukui, and Y. Morimoto Crystallographic study on the interaction of l-lactate oxidase with pyruvate at 1.9 resolution Biochem. Biophys. Res. Commun. 358 2007 1002 1007
45. 2 from Saccharomyces cerevisiae Eur. J. Biochem. 120 1981 279 287
46. K. Stenberg, T. Clausen, Y. Lindqvist, and P. Macheroux Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase Eur. J. Biochem. 228 1995 408 416