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PDBsum entry 1dcc

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Oxidoreductase(h2o2(a)) PDB id
1dcc
Jmol
Contents
Protein chain
291 a.a. *
Ligands
OXY-HEM
Waters ×182
* Residue conservation analysis
PDB id:
1dcc
Name: Oxidoreductase(h2o2(a))
Title: 2.2 angstrom structure of oxyperoxidase: a model for the enzyme:peroxide complex
Structure: CytochromE C peroxidase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Resolution:
2.20Å     R-factor:   0.155    
Authors: M.A.Miller,A.Shaw,J.Kraut
Key ref: M.A.Miller et al. (1994). 2.2 A structure of oxy-peroxidase as a model for the transient enzyme: peroxide complex. Nat Struct Biol, 1, 524-531. PubMed id: 7664080
Date:
01-Jun-94     Release date:   31-Aug-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial
Seq:
Struc:
361 a.a.
291 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.5  - Cytochrome-c peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 ferrocytochrome c + H2O2 = 2 ferricytochrome c + 2 H2O
2 × ferrocytochrome c
+
H(2)O(2)
Bound ligand (Het Group name = OXY)
corresponds exactly
= 2 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     peroxidase activity     2 terms  

 

 
    reference    
 
 
Nat Struct Biol 1:524-531 (1994)
PubMed id: 7664080  
 
 
2.2 A structure of oxy-peroxidase as a model for the transient enzyme: peroxide complex.
M.A.Miller, A.Shaw, J.Kraut.
 
  ABSTRACT  
 
The Fe+3-OOH complex of peroxidases has a very short half life, and its structure cannot be determined by conventional methods. The Fe+2-O2 complex provides a useful structural model for this intermediate, as it differs by only one electron and one proton from the transient Fe+3-OOH complex. We therefore determined the crystal structure of the Fe+2-O2 complex formed by a yeast cytochrome c peroxidase mutant with Trp 191 replaced by Phe. The refined structure shows that dioxygen can form a hydrogen bond with the conserved distal His residue, but not with the conserved distal Arg residue. When the transient Fe+3-OOH complex is modelled in a similar orientation, the active site of peroxidase appears to be optimized for catalysing proton transfer between the vicinal oxygen atoms of the peroxy-anion.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21060958 M.Strianese, A.Varriale, M.Staiano, C.Pellecchia, and S.D'Auria (2011).
Absorption into fluorescence. A method to sense biologically relevant gas molecules.
  Nanoscale, 3, 298-302.  
19139098 X.Zhao, S.Yu, K.Ranguelova, J.Suarez, L.Metlitsky, J.P.Schelvis, and R.S.Magliozzo (2009).
Role of the Oxyferrous Heme Intermediate and Distal Side Adduct Radical in the Catalase Activity of Mycobacterium tuberculosis KatG Revealed by the W107F Mutant.
  J Biol Chem, 284, 7030-7037.  
17339325 C.Lu, T.Egawa, L.M.Wainwright, R.K.Poole, and S.R.Yeh (2007).
Structural and functional properties of a truncated hemoglobin from a food-borne pathogen Campylobacter jejuni.
  J Biol Chem, 282, 13627-13636.  
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
16468033 W.De Jesús-Bonilla, A.Cruz, A.Lewis, J.Cerda, D.E.Bacelo, C.L.Cadilla, and J.López-Garriga (2006).
Hydrogen-bonding conformations of tyrosine B10 tailor the hemeprotein reactivity of ferryl species.
  J Biol Inorg Chem, 11, 334-342.  
12944408 S.Yu, S.Girotto, X.Zhao, and R.S.Magliozzo (2003).
Rapid formation of compound II and a tyrosyl radical in the Y229F mutant of Mycobacterium tuberculosis catalase-peroxidase disrupts catalase but not peroxidase function.
  J Biol Chem, 278, 44121-44127.  
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.  
10769116 B.R.Crane, A.S.Arvai, S.Ghosh, E.D.Getzoff, D.J.Stuehr, and J.A.Tainer (2000).
Structures of the N(omega)-hydroxy-L-arginine complex of inducible nitric oxide synthase oxygenase dimer with active and inactive pterins.
  Biochemistry, 39, 4608-4621.
PDB codes: 1dwv 1dww 1dwx
11114067 C.Jung (2000).
Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy.
  J Mol Recognit, 13, 325-351.  
11102789 F.van Rantwijk, and R.A.Sheldon (2000).
Selective oxygen transfer catalysed by heme peroxidases: synthetic and mechanistic aspects.
  Curr Opin Biotechnol, 11, 554-564.  
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
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.  
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.  
  9514261 Y.Cao, R.A.Musah, S.K.Wilcox, D.B.Goodin, and D.E.McRee (1998).
Protein conformer selection by ligand binding observed with crystallography.
  Protein Sci, 7, 72-78.
PDB code: 1ccj
9030724 J.Bujons, A.Dikiy, J.C.Ferrer, L.Banci, and A.G.Mauk (1997).
Charge reversal of a critical active-site residue of cytochrome-c peroxidase: characterization of the Arg48-->Glu variant.
  Eur J Biochem, 243, 72-84.  
8995273 J.N.Rodriguez-Lopez, A.T.Smith, and R.N.Thorneley (1997).
Effect of distal cavity mutations on the binding and activation of oxygen by ferrous horseradish peroxidase.
  J Biol Chem, 272, 389-395.  
8626735 J.N.Rodriguez-Lopez, A.T.Smith, and R.N.Thorneley (1996).
Role of arginine 38 in horseradish peroxidase. A critical residue for substrate binding and catalysis.
  J Biol Chem, 271, 4023-4030.  
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.