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Crystal structure of catalase HPII from Escherichia coli.

Bravo J, Verdaguer N, Tormo J, Betzel C, Switala J, Loewen PC, Fita I
Structure 3 491-502 (1995)
Cited: 50 times
EuropePMC logo PMID: 7663946

Abstract

Background

Catalase is a ubiquitous enzyme present in both the prokaryotic and eukaryotic cells of aerobic organisms. It serves, in part, to protect the cell from the toxic effects of small peroxides. Escherichia coli produces two catalases, HPI and HPII, that are quite distinct from other catalases in physical structure and catalytic properties. HPII, studied in this work, is encoded by the katE gene, and has been characterized as an oligomeric, monofunctional catalase containing one cis-heme d prosthetic group per subunit of 753 residues.

Results

The crystal structure of catalase HPII from E. coli has been determined to 2.8 A resolution. The asymmetric unit of the crystal contains a whole molecule, which is a tetramer with accurate 222 point group symmetry. In the model built, that includes residues 27-753 and one heme group per monomer, strict non-crystallographic symmetry has been maintained. The crystallographic agreement R-factor is 20.1% for 58,477 reflections in the resolution shell 8.0-2.8 A.

Conclusion

Despite differences in size and chemical properties, which were suggestive of a unique catalase, the deduced structure of HPII is related to the structure of catalase from Penicillium vitale, whose sequence is not yet known. In particular, both molecules have an additional C-terminal domain that is absent in the bovine catalase. This extra domain contains a Rossmann fold but no bound nucleotides have been detected, and its physiological role is unknown. In HPII, the heme group is modified to a heme d and inverted with respect to the orientation determined in all previously reported heme catalases. HPII is the largest catalase for which the structure has been determined to almost atomic resolution.

Reviews - 1iph mentioned but not cited (1)

  1. Monofunctional Heme-Catalases. Hansberg W. Antioxidants (Basel) 11 2173 (2022)

Articles - 1iph mentioned but not cited (4)

  1. Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. Petrova NV, Wu CH. BMC Bioinformatics 7 312 (2006)
  2. CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. Redfern OC, Harrison A, Dallman T, Pearl FM, Orengo CA. PLoS Comput Biol 3 e232 (2007)
  3. Design, synthesis, and evaluation of inhibitors of Norwalk virus 3C protease. Tiew KC, He G, Aravapalli S, Mandadapu SR, Gunnam MR, Alliston KR, Lushington GH, Kim Y, Chang KO, Groutas WC. Bioorg Med Chem Lett 21 5315-5319 (2011)
  4. Discovery of catalases in members of the Chlamydiales order. Rusconi B, Greub G. J Bacteriol 195 3543-3551 (2013)


Reviews citing this publication (4)

  1. Why do bacteria use so many enzymes to scavenge hydrogen peroxide? Mishra S, Imlay J. Arch Biochem Biophys 525 145-160 (2012)
  2. Understanding the structure and function of catalases: clues from molecular evolution and in vitro mutagenesis. Zámocký M, Koller F. Prog Biophys Mol Biol 72 19-66 (1999)
  3. Human catalase: looking for complete identity. Goyal MM, Basak A. Protein Cell 1 888-897 (2010)
  4. Thirty years of heme catalases structural biology. Díaz A, Loewen PC, Fita I, Carpena X. Arch Biochem Biophys 525 102-110 (2012)

Articles citing this publication (41)

  1. Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism. Putnam CD, Arvai AS, Bourne Y, Tainer JA. J Mol Biol 296 295-309 (2000)
  2. Diversity of properties among catalases. Switala J, Loewen PC. Arch Biochem Biophys 401 145-154 (2002)
  3. Proline-dependent oligomerization with arm exchange. Bergdoll M, Remy MH, Cagnon C, Masson JM, Dumas P. Structure 5 391-401 (1997)
  4. Heme proteins--diversity in structural characteristics, function, and folding. Smith LJ, Kahraman A, Thornton JM. Proteins 78 2349-2368 (2010)
  5. A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M. Electrophoresis 27 3306-3321 (2006)
  6. Catalysing new reactions during evolution: economy of residues and mechanism. Bartlett GJ, Borkakoti N, Thornton JM. J Mol Biol 331 829-860 (2003)
  7. Structure of catalase-A from Saccharomyces cerevisiae. Maté MJ, Zamocky M, Nykyri LM, Herzog C, Alzari PM, Betzel C, Koller F, Fita I. J Mol Biol 286 135-149 (1999)
  8. 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)
  9. Structure of catalase HPII from Escherichia coli at 1.9 A resolution. Bravo J, Mate MJ, Schneider T, Switala J, Wilson K, Loewen PC, Fita I. Proteins 34 155-166 (1999)
  10. A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme. Mirts EN, Petrik ID, Hosseinzadeh P, Nilges MJ, Lu Y. Science 361 1098-1101 (2018)
  11. Identification of a novel bond between a histidine and the essential tyrosine in catalase HPII of Escherichia coli. Bravo J, Fita I, Ferrer JC, Ens W, Hillar A, Switala J, Loewen PC. Protein Sci 6 1016-1023 (1997)
  12. Dps-like protein from the hyperthermophilic archaeon Pyrococcus furiosus. Ramsay B, Wiedenheft B, Allen M, Gauss GH, Lawrence CM, Young M, Douglas T. J Inorg Biochem 100 1061-1068 (2006)
  13. Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy. Gouet P, Jouve HM, Williams PA, Andersson I, Andreoletti P, Nussaume L, Hajdu J. Nat Struct Biol 3 951-956 (1996)
  14. Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli. Melik-Adamyan W, Bravo J, Carpena X, Switala J, Maté MJ, Fita I, Loewen PC. Proteins 44 270-281 (2001)
  15. High-level expression of heme-dependent catalase gene katA from Lactobacillus Sakei protects Lactobacillus rhamnosus from oxidative stress. An H, Zhou H, Huang Y, Wang G, Luan C, Mou J, Luo Y, Hao Y. Mol Biotechnol 45 155-160 (2010)
  16. Stereoselective olefin cyclopropanation under aerobic conditions with an artificial enzyme incorporating an iron-chlorin e6 cofactor. Sreenilayam G, Moore EJ, Steck V, Fasan R. ACS Catal 7 7629-7633 (2017)
  17. Activity, peroxide compound formation, and heme d synthesis in Escherichia coli HPII catalase. Obinger C, Maj M, Nicholls P, Loewen P. Arch Biochem Biophys 342 58-67 (1997)
  18. Probing the structure of catalase HPII of Escherichia coli--a review. Loewen P. Gene 179 39-44 (1996)
  19. The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily. Horvath MM, Grishin NV. Proteins 42 230-236 (2001)
  20. Cold adapted features of Vibrio salmonicida catalase: characterisation and comparison to the mesophilic counterpart from Proteus mirabilis. Lorentzen MS, Moe E, Jouve HM, Willassen NP. Extremophiles 10 427-440 (2006)
  21. Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution. Carpena X, Soriano M, Klotz MG, Duckworth HW, Donald LJ, Melik-Adamyan W, Fita I, Loewen PC. Proteins 50 423-436 (2003)
  22. Structure-based functional classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum. Cort JR, Yee A, Edwards AM, Arrowsmith CH, Kennedy MA. J Mol Biol 302 189-203 (2000)
  23. Role of the lateral channel in catalase HPII of Escherichia coli. Sevinc MS, Maté MJ, Switala J, Fita I, Loewen PC. Protein Sci 8 490-498 (1999)
  24. Molecular characterization of a catalase-negative Staphylococcus aureus subsp. aureus Strain collected from a patient with mitral valve endocarditis and pericarditis revealed a novel nonsense mutation in the katA gene. To KK, Cheng VC, Chan JF, Wong AC, Chau S, Tsang FH, Curreem SO, Lau SK, Yuen KY, Woo PC. J Clin Microbiol 49 3398-3402 (2011)
  25. Crystallization and preliminary structural analysis of catalase A from Saccharomyces cerevisiae. Berthet S, Nykyri LM, Bravo J, Mate MJ, Berthet-Colominas C, Alzari PM, Koller F, Fita I. Protein Sci 6 481-483 (1997)
  26. Influence of main channel structure on H(2)O(2) access to the heme cavity of catalase KatE of Escherichia coli. Jha V, Chelikani P, Carpena X, Fita I, Loewen PC. Arch Biochem Biophys 526 54-59 (2012)
  27. The structure and peroxidase activity of a 33-kDa catalase-related protein from Mycobacterium avium ssp. paratuberculosis. Pakhomova S, Gao B, Boeglin WE, Brash AR, Newcomer ME. Protein Sci 18 2559-2568 (2009)
  28. Heme content of recombinant catalase from Psychrobacter sp. T-3 altered by host Escherichia coli cell growth conditions. Kimoto H, Matsuyama H, Yumoto I, Yoshimune K. Protein Expr Purif 59 357-359 (2008)
  29. How catalase recognizes H₂O₂ in a sea of water. Domínguez L, Sosa-Peinado A, Hansberg W. Proteins 82 45-56 (2014)
  30. Hydrolysis of Phosphate Esters Catalyzed by Inorganic Iron Oxide Nanoparticles Acting as Biocatalysts. Huang XL. Astrobiology 18 294-310 (2018)
  31. Preparation and initial characterization of the compound I, II, and III states of iron methylchlorin-reconstituted horseradish peroxidase and myoglobin: models for key intermediates in iron chlorin enzymes. Coulter ED, Cheek J, Ledbetter AP, Chang CK, Dawson JH. Biochem Biophys Res Commun 279 1011-1015 (2000)
  32. Plasma-sensitive Escherichia coli mutants reveal plasma resistance mechanisms. Krewing M, Jarzina F, Dirks T, Schubert B, Benedikt J, Lackmann JW, Bandow JE. J R Soc Interface 16 20180846 (2019)
  33. Structure, recombinant expression and mutagenesis studies of the catalase with oxidase activity from Scytalidium thermophilum. Yuzugullu Y, Trinh CH, Smith MA, Pearson AR, Phillips SE, Sutay Kocabas D, Bakir U, Ogel ZB, McPherson MJ. Acta Crystallogr D Biol Crystallogr 69 398-408 (2013)
  34. Mutation of Phe413 to Tyr in catalase KatE from Escherichia coli leads to side chain damage and main chain cleavage. Jha V, Donald LJ, Loewen PC. Arch Biochem Biophys 525 207-214 (2012)
  35. Availability of Ferritin-Bound Iron to Enterobacteriaceae. Gehrer CM, Hoffmann A, Hilbe R, Grubwieser P, Mitterstiller AM, Talasz H, Fang FC, Meyron-Holtz EG, Atkinson SH, Weiss G, Nairz M. Int J Mol Sci 23 13087 (2022)
  36. Crystallization and preliminary X-ray diffraction analysis of a cold-adapted catalase from Vibrio salmonicida. Riise EK, Lorentzen MS, Helland R, Willassen NP. Acta Crystallogr Sect F Struct Biol Cryst Commun 62 77-79 (2006)
  37. Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs. Jew KM, Le VTB, Amaral K, Ta A, Nguyen May NM, Law M, Adelstein N, Kuhn ML. Front Microbiol 12 805181 (2021)
  38. Ultraviolet-Visible (UV-Vis) and Fluorescence Spectroscopic Investigation of the Interactions of Ionic Liquids and Catalase. Dong X, Fan Y, Yang P, Kong J, Li D, Miao J, Hua S, Hu C. Appl Spectrosc 70 1851-1860 (2016)
  39. Genomic analysis of Paenibacillus sp. MDMC362 from the Merzouga desert leads to the identification of a potentially thermostable catalase. Chemao-Elfihri MW, Hakmi M, Essabbar A, Manni A, Laamarti M, Kartti S, Alouane T, Temsamani L, Eljamali JE, Sbabou L, Aanniz T, Ouadghiri M, Belyamani L, Ibrahimi A, Filali-Maltouf A. Antonie Van Leeuwenhoek 116 21-38 (2023)
  40. Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs. Swain MD, Benson DE. Proteins 59 64-71 (2005)
  41. Studies on metal phthalocyanine as a dual functional mimic enzyme. Feng Q, Liu L, He Y, Wang H, Wu M, Mei F. J Tongji Med Univ 21 13-16 (2001)


Related citations provided by authors (3)

  1. 2.8 A Crystal Structure of Catalase Hpii from Escherichia Coli. Bravo J, Verdaguer N, Tormo J, Betzel C, Switala J, Loewen PC, Fita I Joint Ccp4 Esf-Eacbm Newsletter on Protein Crystallography 28 79- (1993)
  2. Crystallization and Preliminary X-Ray Diffraction Analysis of Catalase Hpii from Escherichia Coli. Tormo J, Fita I, Switala J, Loewen PC J. Mol. Biol. 213 219- (1990)
  3. The Refined Structure of Beef Liver Catalase at 2.5 A Resolution. Fita I, Silva AM, Murthy MRN, Rossmann MG Acta Crystallogr., B 42 497- (1986)

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