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PDBsum entry 1cpf

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Oxidoreductase(h2o2(a)) PDB id
1cpf
Jmol
Contents
Protein chain
291 a.a. *
Ligands
HEM
TRS
Waters ×197
* Residue conservation analysis
PDB id:
1cpf
Name: Oxidoreductase(h2o2(a))
Title: A cation binding motif stabilizes the compound i radical of cytochromE C peroxidase
Structure: CytochromE C peroxidase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Resolution:
2.20Å     R-factor:   0.161    
Authors: M.A.Miller,G.W.Han,J.Kraut
Key ref: M.A.Miller et al. (1994). A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase. Proc Natl Acad Sci U S A, 91, 11118-11122. PubMed id: 7972020 DOI: 10.1073/pnas.91.23.11118
Date:
18-Aug-94     Release date:   01-Nov-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)
= 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: 10.1073/pnas.91.23.11118 Proc Natl Acad Sci U S A 91:11118-11122 (1994)
PubMed id: 7972020  
 
 
A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase.
M.A.Miller, G.W.Han, J.Kraut.
 
  ABSTRACT  
 
Cytochrome c peroxidase reacts with peroxide to form compound I, which contains an oxyferryl heme and an indolyl radical at Trp-191. The indolyl free radical has a half-life of several hours at room temperature, and this remarkable stability is essential for the catalytic function of cytochrome c peroxidase. To probe the protein environment that stabilizes the compound I radical, we used site-directed mutagenesis to replace Trp-191 with Gly or Gln. Crystal structures of these mutants revealed a monovalent cation binding site in the cavity formerly occupied by the side chain of Trp-191. Comparison of this site with those found in other known cation binding enzymes shows that the Trp-191 side chain resides in a consensus K+ binding site. Electrostatic potential calculations indicate that the cation binding site is created by partial negative charges at the backbone carbonyl oxygen atoms of residues 175 and 177, the carboxyl end of a long alpha-helix (residues 165-175), the heme propionates, and the carboxylate side chain of Asp-235. These features create a negative potential that envelops the side chain of Trp-191; the calculated free energy change for cation binding in this site is -27 kcal/mol (1 cal = 4.184J). This is more than sufficient to account for the stability of the Trp-191 radical, which our estimates suggest is stabilized by 7.8 kcal/mol relative to a Trp radical in solution.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
11900539 H.Mei, L.Geren, M.A.Miller, B.Durham, and F.Millett (2002).
Role of the low-affinity binding site in electron transfer from cytochrome C to cytochrome C peroxidase.
  Biochemistry, 41, 3968-3976.  
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
10545195 D.V.Vavilin, S.Y.Ermakova-Gerdes, A.T.Keilty, and W.F.Vermaas (1999).
Tryptophan at position 181 of the D2 protein of photosystem II confers quenching of variable fluorescence of chlorophyll: implications for the mechanism of energy-dependent quenching.
  Biochemistry, 38, 14690-14696.  
10346906 H.Mei, K.Wang, N.Peffer, G.Weatherly, D.S.Cohen, M.Miller, G.Pielak, B.Durham, and F.Millett (1999).
Role of configurational gating in intracomplex electron transfer from cytochrome c to the radical cation in cytochrome c peroxidase.
  Biochemistry, 38, 6846-6854.  
10387007 W.T.Lowther, A.M.Orville, D.T.Madden, S.Lim, D.H.Rich, and B.W.Matthews (1999).
Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis.
  Biochemistry, 38, 7678-7688.
PDB codes: 2mat 3mat 4mat
9485329 D.Sheng, and M.H.Gold (1998).
Irreversible oxidation of ferricytochrome c by lignin peroxidase.
  Biochemistry, 37, 2029-2036.  
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.  
9305956 R.A.Musah, and D.B.Goodin (1997).
Introduction of novel substrate oxidation into cytochrome c peroxidase by cavity complementation: oxidation of 2-aminothiazole and covalent modification of the enzyme.
  Biochemistry, 36, 11665-11674.
PDB code: 1aev
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.  
8555215 J.Wang, R.W.Larsen, S.J.Moench, J.D.Satterlee, D.L.Rousseau, and M.R.Ondrias (1996).
Cytochrome c peroxidase complexed with cytochrome c has an unperturbed heme moiety.
  Biochemistry, 35, 453-463.  
8942678 K.Wang, H.Mei, L.Geren, M.A.Miller, A.Saunders, X.Wang, J.L.Waldner, G.J.Pielak, B.Durham, and F.Millett (1996).
Design of a ruthenium-cytochrome c derivative to measure electron transfer to the radical cation and oxyferryl heme in cytochrome c peroxidase.
  Biochemistry, 35, 15107-15119.  
8673607 M.M.Fitzgerald, R.A.Musah, D.E.McRee, and D.B.Goodin (1996).
A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity.
  Nat Struct Biol, 3, 626-631.
PDB codes: 1aa4 1ac4 1ac8 1aes 1aet 1aeu 1cci 1ryc
  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
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.