Abstract
The crystal structure of horseradish peroxidase isozyme C (HRPC) has been solved to 2.15 Å resolution. An important feature unique to the class III peroxidases is a long insertion, 34 residues in HRPC, between helices F and G. This region, which defines part of the substrate access channel, is not present in the core conserved fold typical of peroxidases from classes I and II. Comparison of HRPC and peanut peroxidase (PNP), the only other class III (higher plant) peroxidase for which an X-ray structure has been completed, reveals that the structure in this region is highly variable even within class III. For peroxidases of the HRPC type, characterized by a larger FG insertion (seven residues relative to PNP) and a shorter F′ helix, we have identified the key residue involved in direct interactions with aromatic donor molecules. HRPC is unique in having a ring of three peripheral Phe residues, 142, 68 and 179. These guard the entrance to the exposed haem edge. We predict that this aromatic region is important for the ability of HRPC to bind aromatic substrates.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Dunford, H.B. Horseradish peroxidase: Structure and Kinetic Properties. In Peroxidases in Chemistry and Biology Vol. 2 (eds Everse, I., Everse, K.E. & Grisham, M. B.) 1–24 (CRC Press, Boca Raton; 1991).
Welinder, K.G. Plant peroxidases: Structure-function relationships. In Plant Peroxidases 1980–1990. Topics and detailed literature on molecular, biochemical and physiological aspects. (eds Penel, C., Gaspar, T. & Greppin H.) 1–24 (University of Geneva, Switzerland; 1992).
Chance, B. The kinetics of the enzyme-substrate compound of peroxidase. J. Biol. Chem. 151, 553–577 (1943).
Poulos, T.L. & Kraut, J. The stereochemistry of peroxidase catalysis J. Biol. Chem. 255, 8199–8205 (1980).
Erman, J.E. et al. Histidine 52 is a critical residue for rapid formation of cytochrome c peroxidase compound I. Biochemistry 32, 9798–9806 (1993).
Vitello, L.B., Erman, J.E., Miller, M.A., Wang, J. & Kraut, J. Effect of Arginine-48 replacement on the reactions between cytochrome c peroxidase and hydrogen peroxide. Biochemistry 32, 9807–9818 (1993).
Rodriguez-Lopez, J.N., Smith, A.T. & Thorneley, R.N.F. Recombinant Horseradish Peroxidase Isoenzyme C: The Effect of Distal Haem Cavity Mutations (His 42→Leu and Arg 38→Leu) on Compound I Formation and Substrate Binding. J. Biol. Inorg. Chem. 1, 136–142 (1996).
Rodriguez-Lopez, J.N., Smith, A.T. & Thorneley, R.N.F. Role of Arg-38 in Horseradish peroxidase. A critical residue for substrate binding and catalysis. J. Biol. Chem. 271, 4023–4030 (1996).
Candeias, L.P., Folkes, L.P., Porssa, M., Parrick, J. & Wardman, P. Rates of reaction of Indoleacetic acids with horseradish peroxidase compound I and their dependence on redox potentials. Biochemistry 35, 102–108 (1996).
Sakurada, J., Sekiguchi, R., Sato, K. & Hosoya, T. Kinetic and molecular orbital studies on the rate of oxidation of monosubstituted phenols and anilines by horseradish peroxidase compound I. Biochemistry 29, 4093–4098 (1990).
Veitch, N.C. & Williams, R.J.P. Two dimensional 1H-NMR studies of horseradish peroxidase C and its interaction with indole-3-propionic acid. Eur. J. Biochem. 189, 351–362 (1990).
Veitch, N.C. & Williams, R.J.P. Two dimensional proton nuclear magnetic resonance studies of plant peroxidase interactions with aromatic donor molecules. In Biochemical, molecular and physiological aspects of plant peroxidases (eds Lobarzewski, J., Greppin, H., Penel, C. & Gaspar, T.) 99–109 (University of Geneva, Switzerland; 1991).
Sakurada, J., Takahashi, S. & Hosoya, T. Nuclear Magnetic Resonance Studies on the Spatial Relationship of Aromatic Donor Molecules to the Heme Iron of Horseradish Peroxidase. J. Biol. Chem. 261, 9657–9662 (1986).
Veitch, N.C., Williams, R.J.P., Bone, N.M., Burke, J.F. & Smith, A.T. Eur. J. Biochem. 233, 650–658 (1995).
Veitch, N.C. & Williams, R.J.P. The use of methylsubstituted benzhydroxamic acids as structural probes of peroxidase substrate binding. Eur. J. Biochem. 229, 629–40 (1995).
Ator, M.A. & Ortiz de Montellano, P.R. Protein control of prosthetic heme reactivity. J.Biol. Chem. 262, 1542–1551 (1987).
Ortiz de Montellano, P.R. Catalytic sites of hemeprotein peroxidases. Annu. Rev. Pharmacol. Toxicol. 32, 89–107 (1992).
Miller, V.P., DePillis, G.D., Ferrer, J.C., Mauk, A.G. & Ortiz de Montellano, P.R. Monooxygenase Activity of Cytochrome c Peroxidase. J. Biol. Chem. 267, 8936–8942 (1992).
Smith, A.T. et al. Expression of a synthetic gene for horseradish peroxidase C in Escherichia coll and folding and activation of the recombinant enzyme with Ca2+ and heme. J. Biol. Chem. 265, 13335–13343 (1990).
Hartmann, C. & Ortiz de Montellano, P.R. Baculovirus expression and characterization of catalytically active horseradish peroxidase. Arch. Biochem. Biophys. 297, 61–72 (1992).
Newmyer, S.L. & Ortiz de Montellano, P.R. Horseradish peroxidase H42A, H42V and F41 A, mutants — histidine catalysis and control of substrate access to the heme iron. J. Biol. Chem. 270, 19430–19438 (1995).
Newmyer, S.L. & Ortiz de Montellano, P.R. Rescue of the catalytic activity of an H42A mutant of horseradish peroxidase by exogenous imidazoles. J. Biol. Chem. 271, 14891–14896 (1996).
Newmyer, S.L., Sun, J., Loehr, T.M. & Ortiz de Montellano, P.R. Rescue of the horseradish peroxidase H170A mutant activity by imidazole - importance of proximal ligand tethering. Biochemistry 35, 12788–12795 (1996).
Rodriguez-Lopez, J.N., Smith, A.T. & Thorneley, R.N. Effect of distal cavity mutations on the binding and activation of oxygen by ferrous horseradish peroxidase. J. Biol. Chem. 272, 389–395 (1997).
Nagano, S., Tanaka, M., Ishimori, K., Watanabe, Y. & Morishima, I. Catalytic roles of the distal site asparagine-histidine couple in peroxidases. Biochemistry 35, 14251–14258 (1996).
Howes, B.D., Rodriguez-Lopez, J.N., Smith, A.T. & Smulevich, G. Mutation of distal residues of horseradish peroxidase: influence on substrate binding and cavity properties. Biochemistry 36, 1532–1543 (1997).
Zhao, D., Gilfoyle, D.J., Smith, A.T. & Loew, G. Refinement of 3D models of Horeseradish peroxidase: Predictions of 2D NMR assignments and substrate binding sites. Prot. Struc. Func. Gen. 26, 204–216 (1996).
Schuller, D.J., Ban, N., van Huystee, R.B., McPherson, A. & Poulos, T.L. The crystal structure of peanut peroxidase. Structure 4, 311–321 (1996).
Simon, P. et al. The peroxidase gene family of Arabidopsis Thaliana. In Plant Peroxidases: Biochemistry and Physiology (eds Obinger, C. et al.) 179–183 (University of Geneva, Switzerland; 1996).
Poulos, T.L., et al., & Kraut, J. The structure of cytochrome C at 2.5 Å resolution. J. Biol. Chem. 255, 575–580 (1980).
Patterson, W.R. & Poulos, T.L. Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry 34, 4331–4341 (1995).
Kunishima, N. et al., & Amachi, T. Crystal structure of the fungal peroxidase from Arthromyces ramocus at 1.9 Å resolution. J. Mol. Biol. 235, 331–344 (1994).
Poulos, T.L., Edwards, S.L., Wariishi, H. & Gold, M.H. Crystallographic refinement of lignin peroxidase at 2 Å. J. Biol. Chem. 268, 4429–4440 (1993).
Piontek, K., Glumoff, T. & Winterhalter, K. Low pH crystal structure of glycosylated lignin peroxidase from Phanerocaete chrysosporium at 2.06 Å resolution. FEBs Lett. 315, 119–124 (1993).
Smith, A.T., Du, P. & Loew, G.H. Homology modeling of horseradish peroxidase. In Nuclear magnetic resonance of paramagnetic macromolecules (ed. La Mar, G.N.) 75–93 (Kluwer Academic Publishers, Dordrecht, Netherlands; 1994).
Jones, A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these maps. Acta Crystallogr. A47, 110–119 (1991).
Welinder, K.G. Amino acid sequence studies of horseradish peroxidase. Eur. J. Biochem. 96, 483–502 (1979).
Hiner, A.N. et al. comparative study of the inactivation of wild-type, recombinant and two mutant horseradish peroxidase isoenzymes C by hydrogen peroxide and m-chloroperoxybenzoic acid. Eur. J. Biochem. 234, 506–512 (1995).
Fukuyama, K., Kunishima, N., Amada, F., Kubota, T. & Matsubara, H. Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. J. Biol. Chem. 270, 21884–21892 (1995).
Smulevich, G. et al. Characterization of recombinant horseradish peroxidase C and three site-directed mutants, F41V, F41W, and R38K, by resonance Raman spectroscopy. Biochemistry 33, 7398–407 (1994).
Smulevich, G., English, A.M., Martini, A.R. & Marzocchi, M.P. Resonance Raman investigation of ferric ion in horseradish peroxidase and its aromatic donor complexes at room and low temperature. Biochemistry 30, 772–779 (1991).
Pappa, H.S. & Cass, A.E. A step towards understanding the folding mechanism of horseradish peroxidase. Tryptophan fluorescence and circular dichroism equilibrium studies. Eur. J. Biochem. 212, 227–235 (1995).
Shiro, Y., Kurono, M. & Morishima, I. Presence of endogenous calcium ion and its functional and structural regulation in horseradish peroxidase. J. Biol. Chem. 261, 9382–9390 (1986).
Welinder, K.G. & Gajhede, M. Structure and Evolution of Peroxidases. Proceedings of : Plant Peroxidases Biochemistry and Physiology. III International Symposium July 10–14 (eds Welinder, K.G., Rasmussen, S.K., Penel, C. & Greppin, H.) 35–42 (University of Geneva, Elsinore, Denmark; 1993).
Veitch, N.C. et al. Structural studies by proton-NMR spectroscopy of plant peroxidase C, the wild-type recombinant protein from Escherichia coli and two protein variants, Phe41 Val and Arg38 Lys. Eur. J. Biochem. 207, 521–531 (1992).
Choudhury, K. et al. Role of the proximal ligand in peroxidase catalysis. Crystallographic, kinetic, and spectral studies of cytochrome c peroxidase proximal ligand mutants. J. Biol. Chem. 269, 20239–20249 (1994).
Mauro, J.M. et al. Tryptophan 191→phenylalanine, a proximal-side mutation in yeast cytochrome c peroxidase that strongly affects the kinetics of ferrocytochrome c oxidation. Biochemistry 27, 6243–6256 (1988).
Sivaraja, M., Goodin, D.B., Smith, M. & Hoffman, B.M. Identification of Trp-191 as free radical site in CCP compound ES. Science 245, 738–740 (1989).
Patterson, W.R., Poulos, T.L. & Goodin, D.B. Identification of a porphyrin-cation radical in ascorbate peroxidase compound I. Biochemistry 34, 4342–4345 (1995).
Veitch, N.C., Gao, Y., Smith, A.T. & White, C.G. Identification of a critical phenyialanine residue in the horseradish peroxidase, Phe 179, by site directed mutagenesis and H-NMR: Implications for complex formation with aromatic donor molecules. Biochemistry (in press) (1997).
Kjalke, M. et al. Comparison of structure and activities of peroxidases from Coprinus cinereus, Coprinus macrorhizus and Arthromyces ramosus. Biochim. Biophys. Acta. 1120, 248–256 (1992).
Braithwaite, A. Unit cell dimensions of crystalline horseradish peroxidase. J. Mol. Biol. 106, 229–230 (1976).
Green, B.N. & Olivier, R.W.A. The study of intact proteins and glycoproteins by electrospray m.s. Biochem. Soc. Trans. 19, 929–935 (1991).
Henriksen, A. et al. Preliminary X-ray Diffraction Studies of Recombinant Peroxidase Isoenzyme C. Acta. Crystallogr. D51, 121–123 (1995).
Otwinowski, Z. Oscillation data reduction program. In Proceedings of the CCP4 study weekend: Data collection and processing 29–30 January 1993 (eds Sawyer, I., Isaacs, N. & Bailey, S.) 56–62 (SERC Daresbury Laboratory, England; 1993).
Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A50, 157–163 (1994).
Matthews, B.W. Solvent content of proteins. J. Mol. Biol. 33, 491–497 (1968).
CCP4, 1994 Collaborative Computing Project, number 4 The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).
Schuller, D.J. MAGICSQUASH: more versatile non-crystallographic averaging with multiple constraints. Acta Crystallogr. D52, 425–434 (1996).
Kleywegt, G.J. & Jones, T.A. Efficient rebuilding of protein structures. Acta. Crystallogr. D52, 829–841 (1996).
Brünger, A.T. X-PLOR Version 3.1. A system for X-ray Crystallography and NMR (Yale University Press, New Haven, Connecticut, USA; 1993).
Engh, R.A. & Huber, R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta. Crystallogr. A47, 392–400 (1991).
Barton, G.J. Protein multiple sequence alignment and flexible pattern matching. Meth. Enz. 183, 403–428 (1990).
Evans, S.V. SETOR: Hardware-lighted three dimensional solid model representations of macromolecules. J. Mol. Graphics 11, 134–138 (1993).
Russell, R.B. & Barton, G.J. Multiple protein sequence alignment from tertiary structure comparison. Proteins 14, 309–323 (1992).
Barton, G.J. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 6, 37–40 (1993).
Humphrey, W., Dalke, A. & Schulten, K. VMD - Visual Molecular Dynamics. J. Molec. Graphics 14, 33–38 (1996).
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Gajhede, M., Schuller, D., Henriksen, A. et al. Crystal structure of horseradish peroxidase C at 2.15 Å resolution. Nat Struct Mol Biol 4, 1032–1038 (1997). https://doi.org/10.1038/nsb1297-1032
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nsb1297-1032
This article is cited by
-
The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development
Molecular Biomedicine (2022)
-
Nanocomposite-based dual enzyme system for broad-spectrum scavenging of reactive oxygen species
Scientific Reports (2021)
-
Immobilization of Horseradish Peroxidase on Modified Cellulose Carriers via Hydrophobic Interactions: Catalytic Properties and Stability
Iranian Journal of Science and Technology, Transactions A: Science (2021)
-
Entrapment of horseradish peroxidase into nanometer-scale metal–organic frameworks: a new nanocarrier for signal amplification in enzyme-linked immunosorbent assay
Microchimica Acta (2021)
-
Screen, Design and Enzymatic Activity Determination of Artificial Microperoxidases
Chemical Research in Chinese Universities (2018)