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PDBsum entry 1jdr

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protein ligands metals links
Oxidoreductase PDB id
1jdr
Jmol
Contents
Protein chain
294 a.a. *
Ligands
HEM
Metals
__K
Waters ×1797
* Residue conservation analysis
PDB id:
1jdr
Name: Oxidoreductase
Title: Crystal structure of a proximal domain potassium binding variant of cytochromE C peroxidase
Structure: CytochromE C peroxidase. Chain: a. Synonym: ccp. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: opbyc. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.50Å     R-factor:   0.197     R-free:   0.234
Authors: C.A.Bonagura,M.Sundaramoorthy,B.Bhaskar,T.L.Poulos
Key ref:
C.A.Bonagura et al. (1999). The effects of an engineered cation site on the structure, activity, and EPR properties of cytochrome c peroxidase. Biochemistry, 38, 5538-5545. PubMed id: 10220341 DOI: 10.1021/bi982996k
Date:
14-Jun-01     Release date:   27-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial
Seq:
Struc:
361 a.a.
294 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 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)
= 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    
 
 
DOI no: 10.1021/bi982996k Biochemistry 38:5538-5545 (1999)
PubMed id: 10220341  
 
 
The effects of an engineered cation site on the structure, activity, and EPR properties of cytochrome c peroxidase.
C.A.Bonagura, M.Sundaramoorthy, B.Bhaskar, T.L.Poulos.
 
  ABSTRACT  
 
Earlier work [Bonagura et al. (1996) Biochemistry 35, 6107] showed that the K+ site found in the proximal pocket of ascorbate peroxidase (APX) could be engineered into cytochrome c peroxidase (CCP). Binding of K+ at the engineered site results in a loss in activity and destabilization of the CCP compound I Trp191 cationic radical owing to long-range electrostatic effects. The engineered CCP mutant crystal structure has been refined to 1.5 A using data obtained at cryogenic temperatures which provides a more detailed basis for comparison with the naturally occurring K+ site in APX. The characteristic EPR signal associated with the Trp191 radical becomes progressively weaker as K+ is added, which correlates well with the loss in enzyme activity as [K+] is increased. These results coupled with stopped-flow studies support our earlier conclusions that the loss in activity and EPR signal is due to destabilization of the Trp191 cationic radical.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
12538891 A.M.Hays, H.B.Gray, and D.B.Goodin (2003).
Trapping of peptide-based surrogates in an artificially created channel of cytochrome c peroxidase.
  Protein Sci, 12, 278-287.  
12644706 C.L.Hunter, R.Maurus, M.R.Mauk, H.Lee, E.L.Raven, H.Tong, N.Nguyen, M.Smith, G.D.Brayer, and A.G.Mauk (2003).
Introduction and characterization of a functionally linked metal ion binding site at the exposed heme edge of myoglobin.
  Proc Natl Acad Sci U S A, 100, 3647-3652.
PDB codes: 1nz2 1nz3 1nz4 1nz5
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.  
10981626 F.Cedrone, A.Ménez, and E.Quéméneur (2000).
Tailoring new enzyme functions by rational redesign.
  Curr Opin Struct Biol, 10, 405-410.  
10608846 C.A.Bonagura, B.Bhaskar, M.Sundaramoorthy, and T.L.Poulos (1999).
Conversion of an engineered potassium-binding site into a calcium-selective site in cytochrome c peroxidase.
  J Biol Chem, 274, 37827-37833.
PDB code: 1krj
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.