The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Oksanen, Esko ^a,e   Blakeley, Matthew P ^a,b   El Hajji, Mohamed ^a,c   Ryde, Ulf ^a,d   Budayova Spano, Monika ^a  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^b INSTITUT LAUE LANGEVIN   (France)

^c SANOFI   (France)

^d LUND UNIVERSITY   (Sweden)

^e EUROPEAN SPALLATION SOURCE ERIC   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

8 HYDROXYXANTHINE; CHLORIDE; UNCLASSIFIED DRUG; URATE; URATE OXIDASE; XANTHINE;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; NEUTRON; PROTON TRANSPORT; QUANTUM CHEMISTRY; STRUCTURE ANALYSIS;

ASPERGILLUS FLAVUS; CATALYSIS; CRYSTALLOGRAPHY; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; NEUTRONS; PROTEIN CONFORMATION; PROTONS; URATE OXIDASE; XANTHINES;

EID: 84899805626     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086651     Document Type: Article

References (30)

1. Kahn K, Serfozo P, Tipton PA (1997) Identification of the True Product of the Urate Oxidase Reaction. J Am Chem Soc 119: 5435-5442. (Pubitemid 27310720)
2. Sarma AD, Serfozo P, Kahn K, Tipton PA (1999) Identification and purification of hydroxyisourate hydrolase, a novel ureide-metabolizing enzyme. J Biol Chem 274: 33863-33865. (Pubitemid 129511711)
3. Kahn K, Tipton PA (1997) Kinetic mechanism and cofactor content of soybean root nodule urate oxidase. Biochemistry 36: 4731-4738. (Pubitemid 27180953)
4. Simic MG, Jovanovich SV (1989) Antioxidation Mechanisms of Uric Acid. J Am Chem Soc 111: 5778-5782.
5. Altarsha M, Castro B, Monard G (2009) Intrinsic reactivity of uric acid with dioxygen: Towards the elucidation of the catalytic mechanism of urate oxidase. Bioorg Chem 37: 111-125.
6. Maples KR, Mason RP (1988) Free radical metabolite of uric acid. J Biol Chem 263: 1709-1712. (Pubitemid 18052118)
7. Colloc'h N, el Hajji M, Bachet B, L'Hermite G, Schiltz M et al. (1997) Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 A resolution. Nat Structr Biol 4: 947-952. (Pubitemid 27479447)
8. Imhoff RD, Power NP, Borrok MJ, Tipton PA (2003) General base catalysis in the urate oxidase reaction: evidence for a novel Thr-Lys catalytic diad. Biochemistry 42: 4094-4100. (Pubitemid 36418302)
9. Gabison L, Chiadmi M, El Hajji M, Castro B, Colloc'h N et al. (2010) Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand. Acta Crystallogr D66: 714-724.
10. Altarsha M (2005) Modélisation du mécanisme catalytique de l'urate oxydase. Chimie Informatique et Theorique PhD: 189.
11. Kahn K, Tipton PA (1998) Spectroscopic characterization of intermediates in the urate oxidase reaction. Biochemistry 37: 11651-11659. (Pubitemid 28388209)
12. Bentley R, Neuberger A (1952) The Mechanism of Action of Uricase. Biochem J 52: 694-699.
13. Gabison L, Chopard C, Colloc'h N, Peyrot F, Castro B et al. (2011) X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase. Proteins 79: 1964-1976.
14. Blakeley M (2009) Neutron macromolecular crystallography. Crystallography Reviews 15: 157-218.
15. Budayova-Spano M, Dauvergne F, Audiffren M, Bactivelane T, Cusack S (2007) A methodology and an instrument for the temperature-controlled optimization of crystal growth. Acta Crystallogr D63: 339-347. (Pubitemid 46438527)
16. Budayova-Spano M, Bonnete F, Ferte N, El Hajji M, Meilleur F et al. (2006) A preliminary neutron diffraction study of rasburicase, a recombinant urate oxidase enzyme, complexed with 8-azaxanthin. Acta Crystallogr F62: 306-309. (Pubitemid 43890627)
17. Oksanen E, Blakeley MP, Bonnete F, Dauvergne MT, Dauvergne F et al. (2009) Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase. Journal of the Royal Society Interface 6 Suppl 5: S599-610.
18. Vagin A, Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Crystallogr 30: 1022-1025. (Pubitemid 127485985)
19. Colloc'h N, Sopkova-de Oliveira Santos J, Retailleau P, Vivares D, Bonnete F et al. (2007) Protein crystallography under xenon and nitrous oxide pressure: comparison with in vivo pharmacology studies and implications for the mechanism of inhaled anesthetic action. Biophys J 92: 217-224. (Pubitemid 46055205)
20. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D53: 240-255. (Pubitemid 27235885)
21. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D66: 213-221.
22. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ et al. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D58: 1948-1954. (Pubitemid 35337293)
23. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D60: 2126-2132. (Pubitemid 41742764)
24. Ryde U (1996) The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combinedquantum chemical and molecular mechanical calculations. J Comput Aided Mol Des 10: 153-164.
25. Ryde U, Olsson MHM (2001) Structure, strain, and reorganization energy of blue copper models in the protein. Int J Quantum Chem 81: 335-347. (Pubitemid 32188302)
26. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J et al. (2008) AMBER 10. San Francisco: University of California.
27. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21: 1049-1074.
28. Schäfer A, Horn H, Ahlrichs R (1992) Fully Optimized Contracted Gaussian Basis Sets for Atoms Li to Kr. J Chem Phys 97: 2571.
29. Schäfer A, Huber C, Ahlrichs R (1994) Fully Optimized Contracted Gaussian Basis Sets of Triple Zeta Valence Quality for Atoms Li to Kr. J Chem Phys 100: 5829.
30. Altarsha M, Monard G, Castro B (2007) Comparative semiempirical and ab initio study of the structural and chemical properties of uric acid and its anions. Int J Quantum Chem 107: 172-181. (Pubitemid 44831379)