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Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase.

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Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA
OpenAccess logo Angew Chem Int Ed Engl 53 13710-4 (2014)
Related entries: 4cw0, 4cw2, 4cw3, 4cw6, 4d13, 4d17, 4d19

Cited: 30 times
EuropePMC logo PMID: 25314114

Abstract

Cofactor-free oxidases and oxygenases promote and control the reactivity of O2 with limited chemical tools at their disposal. Their mechanism of action is not completely understood and structural information is not available for any of the reaction intermediates. Near-atomic resolution crystallography supported by in crystallo Raman spectroscopy and QM/MM calculations showed unambiguously that the archetypical cofactor-free uricase catalyzes uric acid degradation via a C5(S)-(hydro)peroxide intermediate. Low X-ray doses break specifically the intermediate C5-OO(H) bond at 100 K, thus releasing O2 in situ, which is trapped above the substrate radical. The dose-dependent rate of bond rupture followed by combined crystallographic and Raman analysis indicates that ionizing radiation kick-starts both peroxide decomposition and its regeneration. Peroxidation can be explained by a mechanism in which the substrate radical recombines with superoxide transiently produced in the active site.

Articles - 4d12 mentioned but not cited (8)

  1. Glycotope sharing between snail hemolymph and larval schistosomes: larval transformation products alter shared glycan patterns of plasma proteins. Yoshino TP, Wu XJ, Liu H, Gonzalez LA, Deelder AM, Hokke CH. PLoS Negl Trop Dis 6 e1569 (2012)
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  4. Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis. McGregor L, Földes T, Bui S, Moulin M, Coquelle N, Blakeley MP, Rosta E, Steiner RA. IUCrJ 8 46-59 (2021)
  5. Computational Approach for Rational Design of Fusion Uricase with PAS Sequences. Najjari A, Rahimi H, Nojoumi SA, Omidinia E. Int J Mol Cell Med 9 90-103 (2020)
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  7. Schistosoma mansoni egg-derived thioredoxin and Sm14 drive the development of IL-10 producing regulatory B cells. Chayé MAM, Gasan TA, Ozir-Fazalalikhan A, Scheenstra MR, Zawistowska-Deniziak A, van Hengel ORJ, Gentenaar M, Manurung MD, Harvey MR, Codée JDC, Chiodo F, Heijke AM, Kalinowska A, van Diepen A, Hensbergen PJ, Yazdanbakhsh M, Guigas B, Hokke CH, Smits HH. PLoS Negl Trop Dis 17 e0011344 (2023)
  8. The antibodies 3D12 and 4D12 recognise distinct epitopes and conformations of HLA-E. Brackenridge S, John N, Früh K, Borrow P, McMichael AJ. Front Immunol 15 1329032 (2024)


Reviews citing this publication (3)

  1. Radiation damage to macromolecules: kill or cure? Garman EF, Weik M. J Synchrotron Radiat 22 195-200 (2015)
  2. New insight into cofactor-free oxygenation from combined experimental and computational approaches. Bui S, Steiner RA. Curr Opin Struct Biol 41 109-118 (2016)
  3. Radiation chemists look at damage in redox proteins induced by X-rays. Wherland S, Pecht I. Proteins 86 817-826 (2018)

Articles citing this publication (19)

  1. Estimate your dose: RADDOSE-3D. Bury CS, Brooks-Bartlett JC, Walsh SP, Garman EF. Protein Sci 27 217-228 (2018)
  2. Specific radiation damage is a lesser concern at room temperature. Gotthard G, Aumonier S, De Sanctis D, Leonard G, von Stetten D, Royant A. IUCrJ 6 665-680 (2019)
  3. Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution. Clavel D, Gotthard G, von Stetten D, De Sanctis D, Pasquier H, Lambert GG, Shaner NC, Royant A. Acta Crystallogr D Struct Biol 72 1298-1307 (2016)
  4. Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid. Wei D, Huang X, Qiao Y, Rao J, Wang L, Liao F, Zhan CG. ACS Catal 7 4623-4636 (2017)
  5. Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive. Zielinski KA, Prester A, Andaleeb H, Bui S, Yefanov O, Catapano L, Henkel A, Wiedorn MO, Lorbeer O, Crosas E, Meyer J, Mariani V, Domaracky M, White TA, Fleckenstein H, Sarrou I, Werner N, Betzel C, Rohde H, Aepfelbacher M, Chapman HN, Perbandt M, Steiner RA, Oberthuer D. IUCrJ 9 778-791 (2022)
  6. Refining the reaction mechanism of O2 towards its co-substrate in cofactor-free dioxygenases. Silva PJ. PeerJ 4 e2805 (2016)
  7. Quantifying and comparing radiation damage in the Protein Data Bank. Shelley KL, Garman EF. Nat Commun 13 1314 (2022)
  8. Designing a mutant Candida uricase with improved polymerization state and enzymatic activity. Tao L, Li D, Li Y, Shi X, Wang J, Rao C, Zhang Y. Protein Eng Des Sel 30 753-759 (2017)
  9. On the Permeation by Dioxygen of Urate Oxidase from Aspergillus flavus in Complex with Xanthine Anion: Dioxygen Pathways and a Portrait of the Enzyme Cavities from Molecular Dynamics Simulations in Water Solution. Pietra F. Chem Biodivers 13 798-806 (2016)
  10. A role for Vibrio vulnificus PecS during hypoxia. Bhattacharyya N, Lemon TL, Grove A. Sci Rep 9 2797 (2019)
  11. Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the α/β-hydrolase fold. Bui S, Gil-Guerrero S, van der Linden P, Carpentier P, Ceccarelli M, Jambrina PG, Steiner RA. Chem Sci 14 10547-10560 (2023)
  12. From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons. Caramello N, Royant A. Acta Crystallogr D Struct Biol 80 60-79 (2024)
  13. Neutron crystallographic refinement with REFMAC5 from the CCP4 suite. Catapano L, Long F, Yamashita K, Nicholls RA, Steiner RA, Murshudov GN. Acta Crystallogr D Struct Biol 79 1056-1070 (2023)
  14. Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates-Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid. Ortega P, Gil-Guerrero S, González-Sánchez L, Sanz-Sanz C, Jambrina PG. Int J Mol Sci 24 7424 (2023)
  15. Editorial Choosing the optimal spectroscopic toolkit to understand protein function. Hough MA. Biosci Rep 37 BSR20160378 (2017)
  16. Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism. Mori G, Liuzzi A, Ronda L, Di Palma M, Chegkazi MS, Bui S, Garcia-Maya M, Ragazzini J, Malatesta M, Della Monica E, Rivetti C, Antin PB, Bettati S, Steiner RA, Percudani R. Mol Biol Evol 40 msad200 (2023)
  17. Introduction to the virtual thematic issue on room-temperature biological crystallography. Steiner RA. IUCrJ 10 248-250 (2023)
  18. Introduction to the virtual thematic issue on room-temperature biological crystallography. Steiner RA. Acta Crystallogr F Struct Biol Commun 79 79-81 (2023)
  19. Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase. Li K, Fielding EN, Condurso HL, Bruner SD. Acta Crystallogr D Struct Biol 73 573-580 (2017)


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