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Peroxidase(donor:h2o2 oxidoreductase) PDB id
1arp
Jmol
Contents
Protein chain
336 a.a. *
Ligands
NAG-NAG
HEM
Metals
_CA ×2
Waters ×246
* Residue conservation analysis
PDB id:
1arp
Name: Peroxidase(donor:h2o2 oxidoreductase)
Title: Crystal structure of the fungal peroxidase from arthromyces 1.9 angstroms resolution: structural comparisons with the l cytochromE C peroxidases
Structure: Peroxidase. Chain: a. Engineered: yes
Source: Penicillium janthinellum. Penicillium vitale. Organism_taxid: 5079
Resolution:
1.90Å     R-factor:   0.174    
Authors: N.Kunishima,K.Fukuyama
Key ref:
N.Kunishima et al. (1994). Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases. J Mol Biol, 235, 331-344. PubMed id: 8289254 DOI: 10.1016/S0022-2836(05)80037-3
Date:
18-Jun-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28313  (PER_ARTRA) -  Peroxidase
Seq:
Struc: 		364 a.a.
336 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.7  - Peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 phenolic donor + H2O2 = 2 phenoxyl radical of the donor + 2 H2O
2 × phenolic donor
 + H(2)O(2)
 = 2 × phenoxyl radical of the donor
 + 2 × H(2)O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0022-2836(05)80037-3 J Mol Biol 235:331-344 (1994)
PubMed id: 8289254  
 
 
Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases.
N.Kunishima, K.Fukuyama, H.Matsubara, H.Hatanaka, Y.Shibano, T.Amachi.
 
  ABSTRACT  
 
The crystal structure of the peroxidase (donor: H2O2 oxidoreductase, EC 1.11.1.7) from the hyphomycete Arthromyces ramosus (ARP) has been determined by the multiple isomorphous replacement method and refined by the simulated annealing method to a crystallographic R-factor of 17.4% for the 19,191 reflections with F > 2 sigma F between 7.0 and 1.9 A resolution. The model includes residues 9 to 344, the heme group, two N-acetylglucosamine residues, two calcium ions and 246 water molecules. The root-mean-square deviation of bond lengths from the ideal values is 0.02 A. The mean coordinate error is estimated as 0.2 A. The electron density of the glycine-rich region of the amino-terminal eight residues was invisible. ARP has ten major and two short alpha-helices and a few short beta-strands. The overall tertiary structure of ARP is similar to that of yeast cytochrome c peroxidase (CCP) and is particularly similar to that of the lignin peroxidase (LiP) from Phanerochaete chrysosporium. Relative to CCP, ARP and LiP each have an extension of approximately 40 residues at the carboxy terminus. All eight cysteine residues in ARP form disulfide bonds (C12:C24, C23:C293, C43:C129 and C257:C322). Two calcium sites are inaccessible to solvent. The four disulfide bonds and two calcium sites, which are lacking in CCP, are conserved in ARP and LiP. The bond from Asn304C to Ala305N in ARP is the site sensitive to proteases. An Asx turn present in the Asn303 to Ala305 segment appears to orient the side-chain of Asn304 to outward from the molecule, rendering it easily trappable by pockets of proteases. The proximal heme ligand is His184 in helix F (distance of N epsilon 2 ... Fe, 2.10 A), and one of several water molecules in the distal pocket of the heme bridges the iron atom and the N epsilon 2 of His56. The orientation of the imidazole ring of the distal histidine residue relative to the heme group in ARP differs significantly from that in LiP. The access channel to the distal side of the heme of ARP is markedly wider along the heme plane than that of LiP. Many of the amino acid residues that comprise the entrance of this channel differ for ARP and LiP. This may account for the differences in substrate specificity.
 
  Selected figure(s)  
 
Figure 8.
Figur 8. Superposition of ARP and LiP at the heme binding region. Yellow, ARP; blue, LiP. 		Figure 10.
Figure 10. Stereo views of the environments of 2 calcium sites. (a) Site 1; and (b) site 2. The interat~mic distances to site 1 are: D570, 26 A; D570 a~, 25 G750, 26 A; 8790 y, 24 A; D77062, 2-6 ; Watt24, 2-5 A; and War425, 25 A. Those to site 2 are: 81850, 2-5 A; S1850 y, 27 A; D202061, 25 A; D2020 a2, 2-6 A; T2040, 25 A; T20,10 yl, 27 A; V2070, 25 A; and D20906z, 26 A.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1994, 235, 331-344) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19907057 A.K.Singh, R.P.Kumar, N.Pandey, N.Singh, M.Sinha, A.Bhushan, P.Kaur, S.Sharma, and T.P.Singh (2010).
Mode of binding of the tuberculosis prodrug isoniazid to heme peroxidases: binding studies and crystal structure of bovine lactoperoxidase with isoniazid at 2.7 A resolution.
  J Biol Chem, 285, 1569-1576.
PDB codes: 3gc1 3i6n
20495915 M.Hofrichter, R.Ullrich, M.J.Pecyna, C.Liers, and T.Lundell (2010).
New and classic families of secreted fungal heme peroxidases.
  Appl Microbiol Biotechnol, 87, 871-897.  
19465478 A.K.Singh, N.Singh, M.Sinha, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, and T.P.Singh (2009).
Binding modes of aromatic ligands to mammalian heme peroxidases with associated functional implications: crystal structures of lactoperoxidase complexes with acetylsalicylic acid, salicylhydroxamic acid, and benzylhydroxamic acid.
  J Biol Chem, 284, 20311-20318.  
19167310 A.K.Singh, N.Singh, S.Sharma, K.Shin, M.Takase, P.Kaur, A.Srinivasan, and T.P.Singh (2009).
Inhibition of lactoperoxidase by its own catalytic product: crystal structure of the hypothiocyanate-inhibited bovine lactoperoxidase at 2.3-A resolution.
  Biophys J, 96, 646-654.
PDB code: 3bxi
19015819 J.Kulys, Z.Dapkunas, and R.Stupak (2009).
Intensification of biocatalytical processes by synergistic substrate conversion. Fungal peroxidase catalyzed N-hydroxy derivative oxidation in presence of 10-propyl sulfonic acid phenoxazine.
  Appl Biochem Biotechnol, 158, 445-456.  
17372351 K.Fukuyama, and T.Okada (2007).
Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron.
  Acta Crystallogr D Biol Crystallogr, 63, 472-477.
PDB codes: 2e39 2e3a 2e3b
17534526 T.L.Poulos (2007).
The Janus nature of heme.
  Nat Prod Rep, 24, 504-510.  
16791642 G.Battistuzzi, M.Bellei, F.De Rienzo, and M.Sola (2006).
Redox properties of the Fe3+/Fe2+ couple in Arthromyces ramosus class II peroxidase and its cyanide adduct.
  J Biol Inorg Chem, 11, 586-592.  
15326296 P.Pellicena, D.S.Karow, E.M.Boon, M.A.Marletta, and J.Kuriyan (2004).
Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases.
  Proc Natl Acad Sci U S A, 101, 12854-12859.
PDB codes: 1u4h 1u55 1u56
12618432 C.A.Cunha, S.Macieira, J.M.Dias, G.Almeida, L.L.Goncalves, C.Costa, J.Lampreia, R.Huber, J.J.Moura, I.Moura, and M.J.Romão (2003).
Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).
  J Biol Chem, 278, 17455-17465.
PDB code: 1oah
12621034 C.Ciaccio, A.Rosati, G.De Sanctis, F.Sinibaldi, S.Marini, R.Santucci, P.Ascenzi, K.G.Welinder, and M.Coletta (2003).
Relationships of ligand binding, redox properties, and protonation in Coprinus cinereus peroxidase.
  J Biol Chem, 278, 18730-18737.  
12777761 K.Houborg, P.Harris, J.C.Poulsen, P.Schneider, A.Svendsen, and S.Larsen (2003).
The structure of a mutant enzyme of Coprinus cinereus peroxidase provides an understanding of its increased thermostability.
  Acta Crystallogr D Biol Crystallogr, 59, 997.
PDB code: 1ly8
12777760 K.Houborg, P.Harris, J.Petersen, P.Rowland, J.C.Poulsen, P.Schneider, J.Vind, and S.Larsen (2003).
Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase.
  Acta Crystallogr D Biol Crystallogr, 59, 989-996.
PDB codes: 1h3j 1ly9 1lyc 1lyk
12400090 L.Banci, I.Bartalesi, S.Ciofi-Baffoni, and M.Tien (2003).
Unfolding and pH studies on manganese peroxidase: role of heme and calcium on secondary structure stability.
  Biopolymers, 72, 38-47.  
12487424 R.B.van Huystee, Y.Sun, and B.Lige (2002).
A retrospective look at the cationic peanut peroxidase structure.
  Crit Rev Biotechnol, 22, 335-354.  
11121105 A.Celik, P.M.Cullis, M.J.Sutcliffe, R.Sangar, and E.L.Raven (2001).
Engineering the active site of ascorbate peroxidase.
  Eur J Biochem, 268, 78-85.  
11545682 J.Kulys, and A.Ziemys (2001).
A role of proton transfer in peroxidase-catalyzed process elucidated by substrates docking calculations.
  BMC Struct Biol, 1, 3.  
10933820 H.L.Youngs, P.Moënne-Loccoz, T.M.Loehr, and M.H.Gold (2000).
Formation of a bis(histidyl) heme iron complex in manganese peroxidase at high pH and restoration of the native enzyme structure by calcium.
  Biochemistry, 39, 9994.  
10574977 A.Henriksen, A.T.Smith, and M.Gajhede (1999).
The structures of the horseradish peroxidase C-ferulic acid complex and the ternary complex with cyanide suggest how peroxidases oxidize small phenolic substrates.
  J Biol Chem, 274, 35005-35011.
PDB codes: 6atj 7atj
9987124 F.J.Ruiz-Dueñas, M.J.Martínez, and A.T.Martínez (1999).
Molecular characterization of a novel peroxidase isolated from the ligninolytic fungus Pleurotus eryngii.
  Mol Microbiol, 31, 223-235.
PDB code: 1a20
10387022 F.Neri, C.Indiani, B.Baldi, J.Vind, K.G.Welinder, and G.Smulevich (1999).
Role of the distal phenylalanine 54 on the structure, stability, and ligand binding of Coprinus cinereus peroxidase.
  Biochemistry, 38, 7819-7827.  
10187820 S.Camarero, S.Sarkar, F.J.Ruiz-Dueñas, M.J.Martínez, and A.T.Martínez (1999).
Description of a versatile peroxidase involved in the natural degradation of lignin that has both manganese peroxidase and lignin peroxidase substrate interaction sites.
  J Biol Chem, 274, 10324-10330.
PDB codes: 1bqw 1qjr
10103001 S.X.Chen, and P.Schopfer (1999).
Hydroxyl-radical production in physiological reactions. A novel function of peroxidase.
  Eur J Biochem, 260, 726-735.  
10051582 T.Johjima, N.Itoh, M.Kabuto, F.Tokimura, T.Nakagawa, H.Wariishi, and H.Tanaka (1999).
Direct interaction of lignin and lignin peroxidase from Phanerochaete chrysosporium.
  Proc Natl Acad Sci U S A, 96, 1989-1994.  
9609699 A.Henriksen, D.J.Schuller, K.Meno, K.G.Welinder, A.T.Smith, and M.Gajhede (1998).
Structural interactions between horseradish peroxidase C and the substrate benzhydroxamic acid determined by X-ray crystallography.
  Biochemistry, 37, 8054-8060.
PDB code: 2atj
9442067 A.Henriksen, K.G.Welinder, and M.Gajhede (1998).
Structure of barley grain peroxidase refined at 1.9-A resolution. A plant peroxidase reversibly inactivated at neutral pH.
  J Biol Chem, 273, 2241-2248.
PDB code: 1bgp
9442066 C.B.Rasmussen, A.N.Hiner, A.T.Smith, and K.G.Welinder (1998).
Effect of calcium, other ions, and pH on the reactions of barley peroxidase with hydrogen peroxide and fluoride. Control of activity through conformational change.
  J Biol Chem, 273, 2232-2240.  
9485327 G.Tsaprailis, D.W.Chan, and A.M.English (1998).
Conformational states in denaturants of cytochrome c and horseradish peroxidases examined by fluorescence and circular dichroism.
  Biochemistry, 37, 2004-2016.  
  9572923 M.Heinzkill, L.Bech, T.Halkier, P.Schneider, and T.Anke (1998).
Characterization of laccases and peroxidases from wood-rotting fungi (family Coprinaceae).
  Appl Environ Microbiol, 64, 1601-1606.  
9692973 M.I.Savenkova, J.M.Kuo, and P.R.Ortiz de Montellano (1998).
Improvement of peroxygenase activity by relocation of a catalytic histidine within the active site of horseradish peroxidase.
  Biochemistry, 37, 10828-10836.  
9851717 M.Nissum, A.Feis, and G.Smulevich (1998).
Characterization of soybean seed coat peroxidase: resonance Raman evidence for a structure-based classification of plant peroxidases.
  Biospectroscopy, 4, 355-364.  
9609702 M.Nissum, F.Neri, D.Mandelman, T.L.Poulos, and G.Smulevich (1998).
Spectroscopic characterization of recombinant pea cytosolic ascorbate peroxidase: similarities and differences with cytochrome c peroxidase.
  Biochemistry, 37, 8080-8087.  
9485413 M.Tanaka, K.Ishimori, and I.Morishima (1998).
Structural roles of the highly conserved glu residue in the heme distal site of peroxidases.
  Biochemistry, 37, 2629-2638.  
9533688 W.Jentzen, J.G.Ma, and J.A.Shelnutt (1998).
Conservation of the conformation of the porphyrin macrocycle in hemoproteins.
  Biophys J, 74, 753-763.  
9235990 A.K.Abelskov, A.T.Smith, C.B.Rasmussen, H.B.Dunford, and K.G.Welinder (1997).
pH dependence and structural interpretation of the reactions of Coprinus cinereus peroxidase with hydrogen peroxide, ferulic acid, and 2,2'-azinobis.
  Biochemistry, 36, 9453-9463.  
9346287 A.P.Hill, S.Modi, M.J.Sutcliffe, D.D.Turner, D.J.Gilfoyle, A.T.Smith, B.M.Tam, and E.Lloyd (1997).
Chemical, spectroscopic and structural investigation of the substrate-binding site in ascorbate peroxidase.
  Eur J Biochem, 248, 347-354.  
9199803 E.Balog, K.Kis-Petik, J.Fidy, M.Köhler, and J.Friedrich (1997).
Interpretation of multiple Q(0,0) bands in the absorption spectrum of Mg-mesoporphyrin embedded in horseradish peroxidase.
  Biophys J, 73, 397-405.  
9136871 G.Nie, and S.D.Aust (1997).
Spectral changes of lignin peroxidase during reversible inactivation.
  Biochemistry, 36, 5113-5119.  
9038188 K.Fukuyama, K.Sato, H.Itakura, S.Takahashi, and T.Hosoya (1997).
Binding of iodide to Arthromyces ramosus peroxidase investigated with X-ray crystallographic analysis, 1H and 127I NMR spectroscopy, and steady-state kinetics.
  J Biol Chem, 272, 5752-5756.
PDB code: 1gza
9100022 K.Kishi, D.P.Hildebrand, M.Kusters-van Someren, J.Gettemy, A.G.Mauk, and M.H.Gold (1997).
Site-directed mutations at phenylalanine-190 of manganese peroxidase: effects on stability, function, and coordination.
  Biochemistry, 36, 4268-4277.  
9261177 L.M.Landino, B.C.Crews, J.K.Gierse, S.D.Hauser, and L.J.Marnett (1997).
Mutational analysis of the role of the distal histidine and glutamine residues of prostaglandin-endoperoxide synthase-2 in peroxidase catalysis, hydroperoxide reduction, and cyclooxygenase activation.
  J Biol Chem, 272, 21565-21574.  
9406554 M.Gajhede, D.J.Schuller, A.Henriksen, A.T.Smith, and T.L.Poulos (1997).
Crystal structure of horseradish peroxidase C at 2.15 A resolution.
  Nat Struct Biol, 4, 1032-1038.
PDB code: 1atj
9245421 M.Tanaka, K.Ishimori, M.Mukai, T.Kitagawa, and I.Morishima (1997).
Catalytic activities and structural properties of horseradish peroxidase distal His42 --> Glu or Gln mutant.
  Biochemistry, 36, 9889-9898.  
9245411 M.Tanaka, S.Nagano, K.Ishimori, and I.Morishima (1997).
Hydrogen bond network in the distal site of peroxidases: spectroscopic properties of Asn70 --> Asp horseradish peroxidase mutant.
  Biochemistry, 36, 9791-9798.  
8634253 C.A.Bonagura, M.Sundaramoorthy, H.S.Pappa, W.R.Patterson, and T.L.Poulos (1996).
An engineered cation site in cytochrome c peroxidase alters the reactivity of the redox active tryptophan.
  Biochemistry, 35, 6107-6115.  
8718890 C.A.Davey, and R.E.Fenna (1996).
2.3 A resolution X-ray crystal structure of the bisubstrate analogue inhibitor salicylhydroxamic acid bound to human myeloperoxidase: a model for a prereaction complex with hydrogen peroxide.
  Biochemistry, 35, 10967-10973.  
8612649 D.J.Gilfoyle, J.N.Rodriguez-Lopez, and A.T.Smith (1996).
Probing the aromatic-donor-binding site of horseradish peroxidase using site-directed mutagenesis and the suicide substrate phenylhydrazine.
  Eur J Biochem, 236, 714-722.  
  8805539 D.J.Schuller, N.Ban, R.B.Huystee, A.McPherson, and T.L.Poulos (1996).
The crystal structure of peanut peroxidase.
  Structure, 4, 311-321.
PDB code: 1sch
8756714 G.Smulevich, F.Neri, M.P.Marzocchi, and K.G.Welinder (1996).
Versatility of heme coordination demonstrated in a fungal peroxidase. Absorption and resonance Raman studies of Coprinus cinereus peroxidase and the Asp245-->Asn mutant at various pH values.
  Biochemistry, 35, 10576-10585.  
8611540 I.E.Holzbaur, A.M.English, and A.A.Ismail (1996).
FTIR study of the thermal denaturation of horseradish and cytochrome c peroxidases in D2O.
  Biochemistry, 35, 5488-5494.  
8652538 J.W.Tams, and K.G.Welinder (1996).
Unfolding and refolding of Coprinus cinereus peroxidase at high pH, in urea, and at high temperature. Effect of organic and ionic additives on these processes.
  Biochemistry, 35, 7573-7579.  
8798724 M.I.Savenkova, S.L.Newmyer, and P.R.Montellano (1996).
Rescue of His-42 --> Ala horseradish peroxidase by a Phe-41 --> His mutation. Engineering of a surrogate catalytic histidine.
  J Biol Chem, 271, 24598-24603.  
8916924 N.C.Veitch, Y.Gao, and K.G.Welinder (1996).
The Asp245-->Asn mutant of Coprinus cinereus peroxidase. Characterization by 1H-NMR spectroscopy and comparison with the wild-type enzyme.
  Biochemistry, 35, 14370-14380.  
8942679 R.Sinclair, S.Hallam, M.Chen, B.Chance, and L.Powers (1996).
Active site structure in cytochrome c peroxidase and myoglobin mutants: effects of altered hydrogen bonding to the proximal histidine.
  Biochemistry, 35, 15120-15128.  
8841121 S.L.Newmyer, J.Sun, T.M.Loehr, and P.R.Ortiz de Montellano (1996).
Rescue of the horseradish peroxidase His-170-->Ala mutant activity by imidazole: importance of proximal ligand tethering.
  Biochemistry, 35, 12788-12795.  
8663036 S.L.Newmyer, and P.R.de Montellano (1996).
Rescue of the catalytic activity of an H42A mutant of horseradish peroxidase by exogenous imidazoles.
  J Biol Chem, 271, 14891-14896.  
8916910 S.Nagano, M.Tanaka, K.Ishimori, Y.Watanabe, and I.Morishima (1996).
Catalytic roles of the distal site asparagine-histidine couple in peroxidases.
  Biochemistry, 35, 14251-14258.  
8703928 S.Othman, P.Richaud, A.Verméglio, and A.Desbois (1996).
Evidence for a proximal histidine interaction in the structure of cytochromes c in solution: a resonance Raman study.
  Biochemistry, 35, 9224-9234.  
7746145 B.Heym, P.M.Alzari, N.Honoré, and S.T.Cole (1995).
Missense mutations in the catalase-peroxidase gene, katG, are associated with isoniazid resistance in Mycobacterium tuberculosis.
  Mol Microbiol, 15, 235-245.  
7665612 K.Fukuyama, N.Kunishima, F.Amada, T.Kubota, and H.Matsubara (1995).
Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis.
  J Biol Chem, 270, 21884-21892.
PDB codes: 1aru 1arv 1arw 1arx 1ary
7588722 K.R.Barber, M.J.Rodríguez Marañón, G.S.Shaw, and R.B.Van Huystee (1995).
Structural influence of calcium on the heme cavity of cationic peanut peroxidase as determined by 1H-NMR spectroscopy.
  Eur J Biochem, 232, 825-833.  
7851395 P.Limongi, M.Kjalke, J.Vind, J.W.Tams, T.Johansson, and K.G.Welinder (1995).
Disulfide bonds and glycosylation in fungal peroxidases.
  Eur J Biochem, 227, 270-276.  
7642625 S.L.Newmyer, and P.R.Ortiz de Montellano (1995).
Horseradish peroxidase His-42 --> Ala, His-42 --> Val, and Phe-41 --> Ala mutants. Histidine catalysis and control of substrate access to the heme iron.
  J Biol Chem, 270, 19430-19438.  
8749364 T.L.Poulos (1995).
Cytochrome P450.
  Curr Opin Struct Biol, 5, 767-774.  
7629167 V.P.Miller, D.B.Goodin, A.E.Friedman, C.Hartmann, and P.R.Ortiz de Montellano (1995).
Horseradish peroxidase Phe172-->Tyr mutant. Sequential formation of compound I with a porphyrin radical cation and a protein radical.
  J Biol Chem, 270, 18413-18419.  
7731950 F.Johnson, G.H.Loew, and P.Du (1994).
Homology models of two isozymes of manganese peroxidase: prediction of a Mn(II) binding site.
  Proteins, 20, 312-319.  
  7922023 H.Li, and T.L.Poulos (1994).
Structural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures.
  Structure, 2, 461-464.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.