1apx Citations

Crystal structure of recombinant pea cytosolic ascorbate peroxidase.

Biochemistry 34 4331-41 (1995)
Cited: 92 times
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The crystal structure of recombinant pea cytosolic ascorbate peroxidase has been refined to an R = 0.19 for data between 8.0 and 2.2 A resolution and magnitude of F > or = 2 sigma(magnitude of F). The refined model consists of four ascorbate peroxidase monomers consisting of 249 residues per monomer assembled into two homodimers, with one heme group per monomer. The ascorbate peroxidase model confirms that the pea cytosolic enzyme is a noncovalent homodimer held together by a series of ionic interactions arranged around the 2-fold noncrystallographic dimer axis. As expected from the high level of sequence identity (33%), the overall fold of the ascorbate peroxidase monomer closely resembles that of cytochrome c peroxidase. The average root mean square differences for 137 helical alpha-carbon atoms between the four ascorbate peroxidase monomers and cytochrome c peroxidase and for 249 topologically equivalent alpha-carbon atoms are 0.9 and 1.3 A, respectively. The active site structures are also the same, including the hydrogen-bonding interactions between the proximal His ligand, a buried Asp residue, and a Trp residue, whose indole ring is parallel to and in contact with the proximal His ligand just under the heme ring. This proximal Trp residue is thought to be the site of free radical formation in cytochrome c peroxidase compound I and is also essential for enzyme activity. The corresponding Trp in ascorbate peroxidase, Trp179, occupies exactly the same position. The most interesting, and possibly functionally important, difference between the two peroxidases is the presence of a cation binding site in ascorbate peroxidase located approximately 8 A from the alpha-carbon atom of Trp179.

Articles - 1apx 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. The quantum mixed-spin heme state of barley peroxidase: A paradigm for class III peroxidases. Howes BD, Schiodt CB, Welinder KG, Marzocchi MP, Ma JG, Zhang J, Shelnutt JA, Smulevich G. Biophys. J. 77 478-492 (1999)
  3. In silico characterization and homology modeling of thylakoid-bound ascorbate peroxidase from a drought tolerant wheat cultivar. Katiyar A, Lenka SK, Lakshmi K, Chinnusamy V, Bansal KC. Genomics Proteomics Bioinformatics 7 185-193 (2009)
  4. Molecular model of thylakoid membrane bound (SlAPX6) ascorbate peroxidase from Solanum lycopersicum. Tripathi K, Pandey S, Malik M, Sathelly K, Kaul T. Bioinformation 12 44-47 (2016)

Reviews citing this publication (13)

  1. Antioxidant Systems are Regulated by Nitric Oxide-Mediated Post-translational Modifications (NO-PTMs). Begara-Morales JC, Sánchez-Calvo B, Chaki M, Valderrama R, Mata-Pérez C, Padilla MN, Corpas FJ, Barroso JB. Front Plant Sci 7 152 (2016)
  2. Catalase in peroxidase clothing: Interdependent cooperation of two cofactors in the catalytic versatility of KatG. Njuma OJ, Ndontsa EN, Goodwin DC. Arch. Biochem. Biophys. 544 27-39 (2014)
  3. Heme enzyme structure and function. Poulos TL. Chem. Rev. 114 3919-3962 (2014)
  4. Ascorbate peroxidase acts as a novel determiner of redox homeostasis in Leishmania. Adak S, Pal S. Antioxid. Redox Signal. 19 746-754 (2013)
  5. Thirty years of heme peroxidase structural biology. Poulos TL. Arch. Biochem. Biophys. 500 3-12 (2010)
  6. The Janus nature of heme. Poulos TL. Nat Prod Rep 24 504-510 (2007)
  7. Heme to protein linkages in mammalian peroxidases: impact on spectroscopic, redox and catalytic properties. Zederbauer M, Furtmüller PG, Brogioni S, Jakopitsch C, Smulevich G, Obinger C. Nat Prod Rep 24 571-584 (2007)
  8. Active site structure and catalytic mechanisms of human peroxidases. Furtmüller PG, Zederbauer M, Jantschko W, Helm J, Bogner M, Jakopitsch C, Obinger C. Arch. Biochem. Biophys. 445 199-213 (2006)
  9. Plant peroxisomes as a source of signalling molecules. Nyathi Y, Baker A. Biochim. Biophys. Acta 1763 1478-1495 (2006)
  10. Suicide inactivation of peroxidases and the challenge of engineering more robust enzymes. Valderrama B, Ayala M, Vazquez-Duhalt R. Chem. Biol. 9 555-565 (2002)
  11. Substrate binding and catalysis in heme peroxidases. Smith AT, Veitch NC. Curr Opin Chem Biol 2 269-278 (1998)
  12. Understanding heme cavity structure of peroxidases: comparison of electronic absorption and resonance Raman spectra with crystallographic results. Smulevich G. Biospectroscopy 4 S3-17 (1998)
  13. Cytochrome P450. Poulos TL. Curr. Opin. Struct. Biol. 5 767-774 (1995)

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  1. THE WATER-WATER CYCLE IN CHLOROPLASTS: Scavenging of Active Oxygens and Dissipation of Excess Photons. Asada K. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50 601-639 (1999)
  2. Crystal structure of horseradish peroxidase C at 2.15 A resolution. Gajhede M, Schuller DJ, Henriksen A, Smith AT, Poulos TL. Nat. Struct. Biol. 4 1032-1038 (1997)
  3. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Martell JD, Deerinck TJ, Sancak Y, Poulos TL, Mootha VK, Sosinsky GE, Ellisman MH, Ting AY. Nat. Biotechnol. 30 1143-1148 (2012)
  4. The crystal structure of peanut peroxidase. Schuller DJ, Ban N, Huystee RB, McPherson A, Poulos TL. Structure 4 311-321 (1996)
  5. From sequence analysis of three novel ascorbate peroxidases from Arabidopsis thaliana to structure, function and evolution of seven types of ascorbate peroxidase. Jespersen HM, Kjaersgård IV, Ostergaard L, Welinder KG. Biochem. J. 326 ( Pt 2) 305-310 (1997)
  6. An ankyrin repeat-containing protein plays a role in both disease resistance and antioxidation metabolism. Yan J, Wang J, Zhang H. Plant J. 29 193-202 (2002)
  7. Trypanosoma cruzi expresses a plant-like ascorbate-dependent hemoperoxidase localized to the endoplasmic reticulum. Wilkinson SR, Obado SO, Mauricio IL, Kelly JM. Proc. Natl. Acad. Sci. U.S.A. 99 13453-13458 (2002)
  8. The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle. Choinowski T, Blodig W, Winterhalter KH, Piontek K. J. Mol. Biol. 286 809-827 (1999)
  9. Catalase-like activity of horseradish peroxidase: relationship to enzyme inactivation by H2O2. Hernández-Ruiz J, Arnao MB, Hiner AN, García-Cánovas F, Acosta M. Biochem. J. 354 107-114 (2001)
  10. Analysis of the molecular evolutionary history of the ascorbate peroxidase gene family: inferences from the rice genome. Teixeira FK, Menezes-Benavente L, Margis R, Margis-Pinheiro M. J. Mol. Evol. 59 761-770 (2004)
  11. Comparative proteomic approaches for the isolation of proteins interacting with thioredoxin. Marchand C, Le Maréchal P, Meyer Y, Decottignies P. Proteomics 6 6528-6537 (2006)
  12. The 2.0 A resolution crystal structure of prostaglandin H2 synthase-1: structural insights into an unusual peroxidase. Gupta K, Selinsky BS, Kaub CJ, Katz AK, Loll PJ. J. Mol. Biol. 335 503-518 (2004)
  13. Identification of proteins induced or upregulated by Fusarium head blight infection in the spikes of hexaploid wheat (Triticum aestivum). Zhou W, Kolb FL, Riechers DE. Genome 48 770-780 (2005)
  14. Dual regulation of cytosolic ascorbate peroxidase (APX) by tyrosine nitration and S-nitrosylation. Begara-Morales JC, Sánchez-Calvo B, Chaki M, Valderrama R, Mata-Pérez C, López-Jaramillo J, Padilla MN, Carreras A, Corpas FJ, Barroso JB. J. Exp. Bot. 65 527-538 (2014)
  15. Kinetic study of the inactivation of ascorbate peroxidase by hydrogen peroxide. Hiner AN, Rodríguez-López JN, Arnao MB, Lloyd Raven E, García-Cánovas F, Acosta M. Biochem. J. 348 Pt 2 321-328 (2000)
  16. Prokaryotic origins of the non-animal peroxidase superfamily and organelle-mediated transmission to eukaryotes. Passardi F, Bakalovic N, Teixeira FK, Margis-Pinheiro M, Penel C, Dunand C. Genomics 89 567-579 (2007)
  17. The molecular peculiarities of catalase-peroxidases. Zámocký M, Regelsberger G, Jakopitsch C, Obinger C. FEBS Lett. 492 177-182 (2001)
  18. Leishmania major encodes an unusual peroxidase that is a close homologue of plant ascorbate peroxidase: a novel role of the transmembrane domain. Adak S, Datta AK. Biochem. J. 390 465-474 (2005)
  19. Direct interaction of lignin and lignin peroxidase from Phanerochaete chrysosporium. Johjima T, Itoh N, Kabuto M, Tokimura F, Nakagawa T, Wariishi H, Tanaka H. Proc. Natl. Acad. Sci. U.S.A. 96 1989-1994 (1999)
  20. Comparative study on recombinant chloroplastic and cytosolic ascorbate peroxidase isozymes of spinach. Yoshimura K, Ishikawa T, Nakamura Y, Tamoi M, Takeda T, Tada T, Nishimura K, Shigeoka S. Arch. Biochem. Biophys. 353 55-63 (1998)
  21. Nature of the ferryl heme in compounds I and II. Gumiero A, Metcalfe CL, Pearson AR, Raven EL, Moody PC. J. Biol. Chem. 286 1260-1268 (2011)
  22. Detection of a tryptophan radical in the reaction of ascorbate peroxidase with hydrogen peroxide. Hiner AN, Martínez JI, Arnao MB, Acosta M, Turner DD, Lloyd Raven E, Rodríguez-López JN. Eur. J. Biochem. 268 3091-3098 (2001)
  23. Ascorbate peroxidase from rice seedlings: properties of enzyme isoforms, effects of stresses and protective roles of osmolytes. Sharma P, Dubey RS. Plant Sci. 167 541-550 (2004)
  24. Catalase-peroxidase from the cyanobacterium Synechocystis PCC 6803: cloning, overexpression in Escherichia coli, and kinetic characterization. Jakopitsch C, Rüker F, Regelsberger G, Dockal M, Peschek GA, Obinger C. Biol. Chem. 380 1087-1096 (1999)
  25. Common phylogeny of catalase-peroxidases and ascorbate peroxidases. Zámocký M, Janecek S, Koller F. Gene 256 169-182 (2000)
  26. Membrane-bound class III peroxidases: identification, biochemical properties and sequence analysis of isoenzymes purified from maize (Zea mays L.) roots. Mika A, Buck F, Lüthje S. J Proteomics 71 412-424 (2008)
  27. Oxidation of tetrahydrobiopterin by peroxynitrite or oxoferryl species occurs by a radical pathway. Kohnen SL, Mouithys-Mickalad AA, Deby-Dupont GP, Deby CM, Lamy ML, Noels AF. Free Radic. Res. 35 709-721 (2001)
  28. The role of quaternary interactions on the stability and activity of ascorbate peroxidase. Mandelman D, Schwarz FP, Li H, Poulos TL. Protein Sci. 7 2089-2098 (1998)
  29. Kinetic and spectral properties of pea cytosolic ascorbate peroxidase. Marquez LA, Quitoriano M, Zilinskas BA, Dunford HB. FEBS Lett. 389 153-156 (1996)
  30. Distal side tryptophan, tyrosine and methionine in catalase-peroxidases are covalently linked in solution. Jakopitsch C, Kolarich D, Petutschnig G, Furtmüller PG, Obinger C. FEBS Lett. 552 135-140 (2003)
  31. Phylogenetic relationships in class I of the superfamily of bacterial, fungal, and plant peroxidases. Zámocký M. Eur. J. Biochem. 271 3297-3309 (2004)
  32. Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines. Tong W, Williams RJ, Wei Y, Murga LF, Ko J, Ondrechen MJ. Protein Sci. 17 333-341 (2008)
  33. The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase. Fitzgerald MM, Trester ML, Jensen GM, McRee DE, Goodin DB. Protein Sci. 4 1844-1850 (1995)
  34. An inserted loop region of stromal ascorbate peroxidase is involved in its hydrogen peroxide-mediated inactivation. Kitajima S, Tomizawa K, Shigeoka S, Yokota A. FEBS J. 273 2704-2710 (2006)
  35. Characterization of soybean seed coat peroxidase: resonance Raman evidence for a structure-based classification of plant peroxidases. Nissum M, Feis A, Smulevich G. Biospectroscopy 4 355-364 (1998)
  36. Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 A resolution crystallographic study at pH 4.5. Kunishima N, Amada F, Fukuyama K, Kawamoto M, Matsunaga T, Matsubara H. FEBS Lett. 378 291-294 (1996)
  37. Hydrogen peroxide oxidation by catalase-peroxidase follows a non-scrambling mechanism. Vlasits J, Jakopitsch C, Schwanninger M, Holubar P, Obinger C. FEBS Lett. 581 320-324 (2007)
  38. Turning points in the evolution of peroxidase-catalase superfamily: molecular phylogeny of hybrid heme peroxidases. Zámocký M, Gasselhuber B, Furtmüller PG, Obinger C. Cell. Mol. Life Sci. 71 4681-4696 (2014)
  39. The catalytic role of the distal site asparagine-histidine couple in catalase-peroxidases. Jakopitsch C, Auer M, Regelsberger G, Jantschko W, Furtmüller PG, Rüker F, Obinger C. Eur. J. Biochem. 270 1006-1013 (2003)
  40. cDNA clone, fusion expression and purification of the novel gene related to ascorbate peroxidase from Chinese wild Vitis pseudoreticulata in E. coli. Lin L, Wang X, Wang Y. Mol. Biol. Rep. 33 197-206 (2006)
  41. Engineering the proximal heme cavity of catalase-peroxidase. Jakopitsch C, Regelsberger G, Furtmüller PG, Rüker F, Peschek GA, Obinger C. J. Inorg. Biochem. 91 78-86 (2002)
  42. Class I heme peroxidases: characterization of soybean ascorbate peroxidase. Jones DK, Dalton DA, Rosell FI, Raven EL. Arch. Biochem. Biophys. 360 173-178 (1998)
  43. Proton pumping by cytochrome c oxidase is coupled to peroxidase half of its catalytic cycle. Vygodina TV, Capitanio N, Papa S, Konstantinov AA. FEBS Lett. 412 405-409 (1997)
  44. Understanding the roles of strictly conserved tryptophan residues in O2 producing chlorite dismutases. Blanc B, Rodgers KR, Lukat-Rodgers GS, DuBois JL. Dalton Trans 42 3156-3169 (2013)
  45. Converting cytochrome C into a peroxidase-like metalloenzyme by molecular design. Wang ZH, Lin YW, Rosell FI, Ni FY, Lu HJ, Yang PY, Tan XS, Li XY, Huang ZX, Mauk AG. Chembiochem 8 607-609 (2007)
  46. Engineering the active site of ascorbate peroxidase. Celik A, Cullis PM, Sutcliffe MJ, Sangar R, Raven EL. Eur. J. Biochem. 268 78-85 (2001)
  47. Purification and characterization of a hydroperoxidase from the cyanobacterium Synechocystis PCC 6803: identification of its gene by peptide mass mapping using matrix assisted laser desorption ionization time-of-flight mass spectrometry. Regelsberger G, Obinger C, Zoder R, Altmann F, Peschek GA. FEMS Microbiol. Lett. 170 1-12 (1999)
  48. A heme peroxidase with a functional role as an L-tyrosine hydroxylase in the biosynthesis of anthramycin. Connor KL, Colabroy KL, Gerratana B. Biochemistry 50 8926-8936 (2011)
  49. Role of histidine 42 in ascorbate peroxidase. Kinetic analysis of the H42A and H42E variants. Lad L, Mewies M, Basran J, Scrutton NS, Raven EL. Eur. J. Biochem. 269 3182-3192 (2002)
  50. Characterization of the solution reactivity of a basic heme peroxidase from Cucumis sativus. Battistuzzi G, Bellei M, Bortolotti CA, Rocco GD, Leonardi A, Sola M. Arch. Biochem. Biophys. 423 317-331 (2004)
  51. Catalytic oxidation of p-cresol by ascorbate peroxidase. Celik A, Cullis PM, Lloyd Raven E. Arch. Biochem. Biophys. 373 175-181 (2000)
  52. Horseradish peroxidase: partial rescue of the His-42 --> Ala mutant by a concurrent Asn-70 --> Asp mutation. Savenkova MI, Ortiz de Montellano PR. Arch. Biochem. Biophys. 351 286-293 (1998)
  53. Formation and properties of dimeric recombinant horseradish peroxidase in a system of reversed micelles. Gazaryan IG, Klyachko NL, Dulkis YK, Ouporov IV, Levashov AV. Biochem. J. 328 ( Pt 2) 643-647 (1997)
  54. Chemical, spectroscopic and structural investigation of the substrate-binding site in ascorbate peroxidase. Hill AP, Modi S, Sutcliffe MJ, Turner DD, Gilfoyle DJ, Smith AT, Tam BM, Lloyd E. Eur. J. Biochem. 248 347-354 (1997)
  55. Anionic tobacco peroxidase is active at extremely low pH: veratryl alcohol oxidation with a pH optimum of 1.8. Gazarian IG, Lagrimini LM, George SJ, Thorneley RN. Biochem. J. 320 ( Pt 2) 369-372 (1996)
  56. Regulation of intracellular heme trafficking revealed by subcellular reporters. Yuan X, Rietzschel N, Kwon H, Walter Nuno AB, Hanna DA, Phillips JD, Raven EL, Reddi AR, Hamza I. Proc. Natl. Acad. Sci. U.S.A. 113 E5144-52 (2016)
  57. Divergent evolutionary lines of fungal cytochrome c peroxidases belonging to the superfamily of bacterial, fungal and plant heme peroxidases. Zámocký M, Dunand C. FEBS Lett. 580 6655-6664 (2006)
  58. Nucleotide sequence analysis, overexpression in Escherichia coli and kinetic characterization of Anacystis nidulans catalase-peroxidase. Engleder M, Regelsberger G, Jakopitsch C, Furtmüller PG, Rüker F, Peschek GA, Obinger C. Biochimie 82 211-219 (2000)
  59. Molecular modeling of peroxidase and polyphenol oxidase: substrate specificity and active site comparison. Nokthai P, Lee VS, Shank L. Int J Mol Sci 11 3266-3276 (2010)
  60. Apolar distal pocket mutants of yeast cytochrome c peroxidase: hydrogen peroxide reactivity and cyanide binding of the TriAla, TriVal, and TriLeu variants. Bidwai AK, Meyen C, Kilheeney H, Wroblewski D, Vitello LB, Erman JE. Biochim. Biophys. Acta 1834 137-148 (2013)
  61. Isolation and characterization of two peroxidases from Cucumis sativus. Battistuzzi G, D'Onofrio M, Loschi L, Sola M. Arch. Biochem. Biophys. 388 100-112 (2001)
  62. Cloning, expression and functional validation of drought inducible ascorbate peroxidase (Ec-apx1) from Eleusine coracana. Bhatt D, Saxena SC, Jain S, Dobriyal AK, Majee M, Arora S. Mol. Biol. Rep. 40 1155-1165 (2013)
  63. Role of C-terminal acidic cluster in stabilization of heme spin state of ascorbate peroxidase from Leishmania major. Yadav RK, Dolai S, Pal S, Adak S. Arch. Biochem. Biophys. 495 129-135 (2010)
  64. Evidences for structural basis of altered ascorbate peroxidase activity in cadmium-stressed rice plants exposed to jasmonate. Singh I, Shah K. Biometals 27 247-263 (2014)
  65. Crystal structure analysis of peroxidase from the palm tree Chamaerops excelsa. Bernardes A, Textor LC, Santos JC, Cuadrado NH, Kostetsky EY, Roig MG, Bavro VN, Muniz JR, Shnyrov VL, Polikarpov I. Biochimie 111 58-69 (2015)
  66. Quantum mechanical modeling: a tool for the understanding of enzyme reactions. Náray-Szabó G, Oláh J, Krámos B. Biomolecules 3 662-702 (2013)
  67. Heterologous expression and characterization of a proxidomal ascorbate peroxidase from Populus tomentosa. Lu H, Han RL, Jiang XN. Mol. Biol. Rep. 36 21-27 (2009)
  68. Role of proximal methionine residues in Leishmania major peroxidase. Yadav RK, Pal S, Dolai S, Adak S. Arch. Biochem. Biophys. 515 21-27 (2011)
  69. Inactivation of myeloperoxidase by benzoic acid hydrazide. Huang J, Smith F, Panizzi JR, Goodwin DC, Panizzi P. Arch. Biochem. Biophys. 570 14-22 (2015)
  70. Probing the function of Mycobacterium tuberculosis catalase-peroxidase by site-directed mutagenesis. Eady NA, Jesmin NA, Servos S, Cass AE, Nagy JM, Brown KA. Dalton Trans 3495-3500 (2005)
  71. Influence of plant secondary metabolites on in vitro oxidation of methyl ferulate with cell wall peroxidases from lupine apoplast. Marczak Ł, Wojtaszek P, Stobiecki M. J. Plant Physiol. 165 239-250 (2008)
  72. Luffa aegyptiaca (Gourd) Fruit Juice as a Source of Peroxidase. Yadav RS, Yadav KS, Yadav HS. Enzyme Res 2011 319105 (2011)
  73. Heterolytic OO bond cleavage: Functional role of Glu113 during bis-Fe(IV) formation in MauG. Geng J, Huo L, Liu A. J. Inorg. Biochem. 167 60-67 (2017)
  74. Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Martell JD, Deerinck TJ, Lam SS, Ellisman MH, Ting AY. Nat Protoc 12 1792-1816 (2017)
  75. Optimizing the fragment complementation of APEX2 for detection of specific protein-protein interactions in live cells. Xue M, Hou J, Wang L, Cheng D, Lu J, Zheng L, Xu T. Sci Rep 7 12039 (2017)

Related citations provided by authors (1)

  1. Characterization and Crystallization of Recombinant Pea Cytosolic Ascorbate Peroxidase. Patterson WR, Poulos TL J. Biol. Chem. 269 17020- (1994)