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The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.

Murshudov GN, Grebenko AI, Brannigan JA, Antson AA, Barynin VV, Dodson GG, Dauter Z, Wilson KS, Melik-Adamyan WR
Acta Crystallogr D Biol Crystallogr 58 1972-82 (2002)
Related entries: 1gwe, 1gwh

Cited: 24 times
EuropePMC logo PMID: 12454454

Abstract

The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.

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Reviews citing this publication (6)

  1. Heme enzyme structure and function. Poulos TL. Chem. Rev. 114 3919-3962 (2014)
  2. On the status of ferryl protonation. Behan RK, Green MT. J. Inorg. Biochem. 100 448-459 (2006)
  3. Classical catalase: ancient and modern. Nicholls P. Arch. Biochem. Biophys. 525 95-101 (2012)
  4. The reaction mechanisms of heme catalases: an atomistic view by ab initio molecular dynamics. Alfonso-Prieto M, Vidossich P, Rovira C. Arch. Biochem. Biophys. 525 121-130 (2012)
  5. The influence of X-rays on the structural studies of peroxide-derived myoglobin intermediates. Hersleth HP, Hsiao YW, Ryde U, Görbitz CH, Andersson KK. Chem. Biodivers. 5 2067-2089 (2008)
  6. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Chem. Rev. 118 10840-11022 (2018)

Articles citing this publication (16)

  1. The backrub motion: how protein backbone shrugs when a sidechain dances. Davis IW, Arendall WB, Richardson DC, Richardson JS. Structure 14 265-274 (2006)
  2. Resonance Raman spectroscopy of oxoiron(IV) porphyrin pi-cation radical and oxoiron(IV) hemes in peroxidase intermediates. Terner J, Palaniappan V, Gold A, Weiss R, Fitzgerald MM, Sullivan AM, Hosten CM. J. Inorg. Biochem. 100 480-501 (2006)
  3. Unusual Cys-Tyr covalent bond in a large catalase. Díaz A, Horjales E, Rudiño-Piñera E, Arreola R, Hansberg W. J. Mol. Biol. 342 971-985 (2004)
  4. Crystallographic and spectroscopic studies of peroxide-derived myoglobin compound II and occurrence of protonated FeIV O. Hersleth HP, Uchida T, Røhr AK, Teschner T, Schünemann V, Kitagawa T, Trautwein AX, Görbitz CH, Andersson KK. J Biol Chem 282 23372-23386 (2007)
  5. Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1. Patrauchan MA, Florizone C, Eapen S, Gómez-Gil L, Sethuraman B, Fukuda M, Davies J, Mohn WW, Eltis LD. J. Bacteriol. 190 37-47 (2008)
  6. X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative. Newcomb M, Halgrimson JA, Horner JH, Wasinger EC, Chen LX, Sligar SG. Proc. Natl. Acad. Sci. U.S.A. 105 8179-8184 (2008)
  7. Structure, protonation state and dynamics of catalase compound II. Rovira C. Chemphyschem 6 1820-1826 (2005)
  8. Ultrahigh (0.93A) resolution structure of manganese peroxidase from Phanerochaete chrysosporium: implications for the catalytic mechanism. Sundaramoorthy M, Gold MH, Poulos TL. J. Inorg. Biochem. 104 683-690 (2010)
  9. HTHP: a novel class of hexameric, tyrosine-coordinated heme proteins. Jeoung JH, Pippig DA, Martins BM, Wagener N, Dobbek H. J. Mol. Biol. 368 1122-1131 (2007)
  10. Spectroscopic description of an unusual protonated ferryl species in the catalase from Proteus mirabilis and density functional theory calculations on related models. Consequences for the ferryl protonation state in catalase, peroxidase and chloroperoxidase. Horner O, Mouesca JM, Solari PL, Orio M, Oddou JL, Bonville P, Jouve HM. J. Biol. Inorg. Chem. 12 509-525 (2007)
  11. New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. Prisant MG, Williams CJ, Chen VB, Richardson JS, Richardson DC. Protein Sci 29 315-329 (2020)
  12. Mössbauer identification of a protonated ferryl species in catalase from Proteus mirabilis: density functional calculations on related models. Horner O, Oddou JL, Mouesca JM, Jouve HM. J. Inorg. Biochem. 100 477-479 (2006)
  13. Purification, cloning, expression, and biochemical characterization of a monofunctional catalase, KatP, from Pigmentiphaga sp. DL-8. Dong W, Hou Y, Li S, Wang F, Zhou J, Li Z, Wang Y, Huang F, Fu L, Huang Y, Cui Z. Protein Expr. Purif. 108 54-61 (2015)
  14. Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans. Borges PT, Frazão C, Miranda CS, Carrondo MA, Romão CV. FEBS J. 281 4138-4150 (2014)
  15. Spectroscopic Investigations of Catalase Compound II: Characterization of an Iron(IV) Hydroxide Intermediate in a Non-thiolate-Ligated Heme Enzyme. Yosca TH, Langston MC, Krest CM, Onderko EL, Grove TL, Livada J, Green MT. J. Am. Chem. Soc. 138 16016-16023 (2016)
  16. Structural analysis of NADPH depleted bovine liver catalase and its inhibitor complexes. Sugadev R, Ponnuswamy MN, Sekar K. Int J Biochem Mol Biol 2 67-77 (2011)


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