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PDBsum entry 1apx

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protein ligands metals Protein-protein interface(s) links
Peroxidase PDB id
1apx
Jmol
Contents
Protein chains
249 a.a. *
Ligands
HEM ×4
Metals
__K ×4
Waters ×645
* Residue conservation analysis
PDB id:
1apx
Name: Peroxidase
Title: Crystal structure of recombinant ascorbate peroxidase
Structure: Cytosolic ascorbate peroxidase. Chain: a, b, c, d. Engineered: yes
Source: Pisum sativum. Pea. Organism_taxid: 3888. Gene: cdna. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.20Å     R-factor:   0.193    
Authors: W.R.Patterson,T.L.Poulos
Key ref:
W.R.Patterson and T.L.Poulos (1995). Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry, 34, 4331-4341. PubMed id: 7703247 DOI: 10.1021/bi00013a023
Date:
01-Feb-95     Release date:   08-Mar-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P48534  (APX1_PEA) -  L-ascorbate peroxidase, cytosolic
Seq:
Struc:
250 a.a.
249 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.11  - L-ascorbate peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 L-ascorbate + H2O2 + 2 H+ = L-ascorbate + L-dehydroascorbate + 2 H2O
2 × L-ascorbate
+ H(2)O(2)
+ 2 × H(+)
= L-ascorbate
+ L-dehydroascorbate
+ 2 × H(2)O
      Cofactor: Heme
Heme
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi00013a023 Biochemistry 34:4331-4341 (1995)
PubMed id: 7703247  
 
 
Crystal structure of recombinant pea cytosolic ascorbate peroxidase.
W.R.Patterson, T.L.Poulos.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20957092 P.Nokthai, V.S.Lee, and L.Shank (2010).
Molecular modeling of peroxidase and polyphenol oxidase: substrate specificity and active site comparison.
  Int J Mol Sci, 11, 3266-3276.  
17899442 H.Lu, R.L.Han, and X.N.Jiang (2009).
Heterologous expression and characterization of a proxidomal ascorbate peroxidase from Populus tomentosa.
  Mol Biol Rep, 36, 21-27.  
18096640 W.Tong, R.J.Williams, Y.Wei, L.F.Murga, J.Ko, and M.J.Ondrechen (2008).
Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines.
  Protein Sci, 17, 333-341.  
17534531 M.Zederbauer, P.G.Furtmüller, S.Brogioni, C.Jakopitsch, G.Smulevich, and C.Obinger (2007).
Heme to protein linkages in mammalian peroxidases: impact on spectroscopic, redox and catalytic properties.
  Nat Prod Rep, 24, 571-584.  
17534526 T.L.Poulos (2007).
The Janus nature of heme.
  Nat Prod Rep, 24, 504-510.  
17328023 Z.H.Wang, Y.W.Lin, F.I.Rosell, F.Y.Ni, H.J.Lu, P.Y.Yang, X.S.Tan, X.Y.Li, Z.X.Huang, and A.G.Mauk (2007).
Converting cytochrome C into a peroxidase-like metalloenzyme by molecular design.
  Chembiochem, 8, 607-609.  
17163439 C.Marchand, P.Le Maréchal, Y.Meyer, and P.Decottignies (2006).
Comparative proteomic approaches for the isolation of proteins interacting with thioredoxin.
  Proteomics, 6, 6528-6537.  
16850189 L.Lin, X.Wang, and Y.Wang (2006).
cDNA clone, fusion expression and purification of the novel gene related to ascorbate peroxidase from Chinese wild Vitis pseudoreticulata in E. coli.
  Mol Biol Rep, 33, 197-206.  
16817898 S.Kitajima, K.Tomizawa, S.Shigeoka, and A.Yokota (2006).
An inserted loop region of stromal ascorbate peroxidase is involved in its hydrogen peroxide-mediated inactivation.
  FEBS J, 273, 2704-2710.  
16315359 N.A.Eady, N.A.Jesmin, S.Servos, A.E.Cass, J.M.Nagy, and K.A.Brown (2005).
Probing the function of Mycobacterium tuberculosis catalase-peroxidase by site-directed mutagenesis.
  Dalton Trans, (), 3495-3500.  
15291807 M.Zámocký (2004).
Phylogenetic relationships in class I of the superfamily of bacterial, fungal, and plant peroxidases.
  Eur J Biochem, 271, 3297-3309.  
15231844 R.Pierattelli, L.Banci, N.A.Eady, J.Bodiguel, J.N.Jones, P.C.Moody, E.L.Raven, B.Jamart-Grégoire, and K.A.Brown (2004).
Enzyme-catalyzed mechanism of isoniazid activation in class I and class III peroxidases.
  J Biol Chem, 279, 39000-39009.  
15231843 T.Bertrand, N.A.Eady, J.N.Jones, Jesmin, J.M.Nagy, B.Jamart-Grégoire, E.L.Raven, and K.A.Brown (2004).
Crystal structure of Mycobacterium tuberculosis catalase-peroxidase.
  J Biol Chem, 279, 38991-38999.
PDB code: 1sj2
12603334 C.Jakopitsch, M.Auer, G.Regelsberger, W.Jantschko, P.G.Furtmüller, F.Rüker, and C.Obinger (2003).
The catalytic role of the distal site asparagine-histidine couple in catalase-peroxidases.
  Eur J Biochem, 270, 1006-1013.  
12640445 K.H.Sharp, M.Mewies, P.C.Moody, and E.L.Raven (2003).
Crystal structure of the ascorbate peroxidase-ascorbate complex.
  Nat Struct Biol, 10, 303-307.
PDB codes: 1oaf 1oag
11862948 J.Yan, J.Wang, and H.Zhang (2002).
An ankyrin repeat-containing protein plays a role in both disease resistance and antioxidation metabolism.
  Plant J, 29, 193-202.  
11856855 K.Wada, T.Tada, Y.Nakamura, Y.Yabuta, K.Yoshimura, T.Takeda, S.Shigeoka, and K.Nishimura (2002).
Crystallization and preliminary X-ray diffraction analysis of chloroplastic ascorbate peroxidase of tobacco plants.
  Acta Crystallogr D Biol Crystallogr, 58, 559-561.  
12084058 L.Lad, M.Mewies, J.Basran, N.S.Scrutton, and E.L.Raven (2002).
Role of histidine 42 in ascorbate peroxidase. Kinetic analysis of the H42A and H42E variants.
  Eur J Biochem, 269, 3182-3192.  
12506974 S.Kitajima, M.Ueda, S.Sano, C.Miyake, T.Kohchi, K.Tomizawa, S.Shigeoka, and A.Yokota (2002).
Stable form of ascorbate peroxidase from the red alga Galdieria partita similar to both chloroplastic and cytosolic isoforms of higher plants.
  Biosci Biotechnol Biochem, 66, 2367-2375.  
12351682 S.R.Wilkinson, S.O.Obado, I.L.Mauricio, and J.M.Kelly (2002).
Trypanosoma cruzi expresses a plant-like ascorbate-dependent hemoperoxidase localized to the endoplasmic reticulum.
  Proc Natl Acad Sci U S A, 99, 13453-13458.  
12172540 Y.Yamada, T.Fujiwara, T.Sato, N.Igarashi, and N.Tanaka (2002).
The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui.
  Nat Struct Biol, 9, 691-695.
PDB code: 1itk
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.  
11358529 A.N.Hiner, J.I.Martínez, M.B.Arnao, M.Acosta, D.D.Turner, E.Lloyd Raven, and J.N.Rodríguez-López (2001).
Detection of a tryptophan radical in the reaction of ascorbate peroxidase with hydrogen peroxide.
  Eur J Biochem, 268, 3091-3098.  
10924154 E.Monzani, G.Alzuet, L.Casella, C.Redaelli, C.Bassani, A.M.Sanangelantoni, M.Gullotti, L.de Gioia, L.Santagostini, and F.Chillemi (2000).
Properties and reactivity of myoglobin reconstituted with chemically modified protohemin complexes.
  Biochemistry, 39, 9571-9582.  
10863004 M.Engleder, G.Regelsberger, C.Jakopitsch, P.G.Furtmüller, F.Rüker, G.A.Peschek, and C.Obinger (2000).
Nucleotide sequence analysis, overexpression in Escherichia coli and kinetic characterization of Anacystis nidulans catalase-peroxidase.
  Biochimie, 82, 211-219.  
10821663 S.E.Rigby, S.Jünemann, P.R.Rich, and P.Heathcote (2000).
Reaction of bovine cytochrome c oxidase with hydrogen peroxide produces a tryptophan cation radical and a porphyrin cation radical.
  Biochemistry, 39, 5921-5928.  
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
10220341 C.A.Bonagura, M.Sundaramoorthy, B.Bhaskar, and T.L.Poulos (1999).
The effects of an engineered cation site on the structure, activity, and EPR properties of cytochrome c peroxidase.
  Biochemistry, 38, 5538-5545.
PDB code: 1jdr
10543446 C.Jakopitsch, F.Rüker, G.Regelsberger, M.Dockal, G.A.Peschek, and C.Obinger (1999).
Catalase-peroxidase from the cyanobacterium Synechocystis PCC 6803: cloning, overexpression in Escherichia coli, and kinetic characterization.
  Biol Chem, 380, 1087-1096.  
9919646 G.Regelsberger, C.Obinger, R.Zoder, F.Altmann, and G.A.Peschek (1999).
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.
  FEMS Microbiol Lett, 170, 1.  
15012221 K.Asada (1999).
THE WATER-WATER CYCLE IN CHLOROPLASTS: Scavenging of Active Oxygens and Dissipation of Excess Photons.
  Annu Rev Plant Physiol Plant Mol Biol, 50, 601-639.  
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.  
9915818 T.Matsui, S.Ozaki, E.Liong, G.N.Phillips, and Y.Watanabe (1999).
Effects of the location of distal histidine in the reaction of myoglobin with hydrogen peroxide.
  J Biol Chem, 274, 2838-2844.
PDB codes: 1ofj 1ofk
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
9667928 A.T.Smith, and N.C.Veitch (1998).
Substrate binding and catalysis in heme peroxidases.
  Curr Opin Chem Biol, 2, 269-278.  
  9792095 D.Mandelman, F.P.Schwarz, H.Li, and T.L.Poulos (1998).
The role of quaternary interactions on the stability and activity of ascorbate peroxidase.
  Protein Sci, 7, 2089-2098.  
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.  
9720218 I.J.Kim, and W.I.Chung (1998).
Isolation of genomic DNA containing a cytosolic ascorbate peroxidase gene (ApxSC) from the strawberry (Fragaria x ananassa).
  Biosci Biotechnol Biochem, 62, 1358-1363.  
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.  
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.  
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.  
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.  
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
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.  
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.  
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.  
  8528082 M.M.Fitzgerald, M.L.Trester, G.M.Jensen, D.E.McRee, and D.B.Goodin (1995).
The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase.
  Protein Sci, 4, 1844-1850.
PDB codes: 1cmt 1cmu
8749364 T.L.Poulos (1995).
Cytochrome P450.
  Curr Opin Struct Biol, 5, 767-774.  
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 code is shown on the right.

 

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