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PDBsum entry 1cyf
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Oxidoreductase (h2o2(a)) PDB id
1cyf

 

 

 

 

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Contents
Protein chain
296 a.a. *
Ligands
HEM
Waters ×152
* Residue conservation analysis
PDB id:
1cyf
Name: Oxidoreductase (h2o2(a))
Title: Identifying the physiological electron transfer site of cytochromE C peroxidase by structure-based engineering
Structure: CytochromE C peroxidase. Chain: a. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.35Å     R-factor:   0.166    
Authors: M.A.Miller,G.W.Han,J.Kraut
Key ref:
M.A.Miller et al. (1996). Identifying the physiological electron transfer site of cytochrome c peroxidase by structure-based engineering. Biochemistry, 35, 667-673. PubMed id: 8547245 DOI: 10.1021/bi952557a
Date:
03-Jul-95     Release date:   07-Dec-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		361 a.a.
296 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.5  - cytochrome-c peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 Fe(II)-[cytochrome c] + H2O2 + 2 H+ = 2 Fe(III)-[cytochrome c] + 2 H2O
2 × Fe(II)-[cytochrome c]
 + H2O2
 + 2 × H(+)
 = 2 × Fe(III)-[cytochrome c]
 + 2 × H2O
      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

 

 
    Added reference    
 
 
DOI no: 10.1021/bi952557a Biochemistry 35:667-673 (1996)
PubMed id: 8547245  
 
 
Identifying the physiological electron transfer site of cytochrome c peroxidase by structure-based engineering.
M.A.Miller, L.Geren, G.W.Han, A.Saunders, J.Beasley, G.J.Pielak, B.Durham, F.Millett, J.Kraut.
 
  ABSTRACT  
 
A technique was developed to evaluate whether electron transfer (ET) complexes formed in solution by the cloned cytochrome c peroxidase [CcP(MI)] and cytochromes c from yeast (yCc) and horse (hCc) are structurally similar to those seen in the respective crystal structures. Site-directed mutagenesis was used to convert the sole Cys of the parent enzyme (Cys 128) to Ala, and a Cys residue was introduced at position 193 of CcP(MI), the point of closest contact between CcP(MI) and yCc in the crystal structure. Cys 193 was then modified with a bulky sulfhydryl reagent, 3-(N-maleimidylpropionyl)-biocytin (MPB), to prevent yCc from binding at the site seen in the crystal. The MPB modification has no effect on overall enzyme structure but causes 20-100-fold decreases in transient and steady-state ET reaction rates with yCc. The MPB modification causes only 2-3-fold decreases in ET reaction rates with hCc, however. This differential effect is predicted by modeling studies based on the crystal structures and indicates that solution phase ET complexes closely resemble the crystalline complexes. The low rate of catalysis of the MPB-enzyme was constant for yCc in buffers of 20-160 mM ionic strength. This indicates that the low affinity complex formed between CcP(MI) and yCc at low ionic strength is not reactive in ET.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19072042 A.M.Hays Putnam, Y.T.Lee, and D.B.Goodin (2009).
Replacement of an electron transfer pathway in cytochrome c peroxidase with a surrogate peptide.
  Biochemistry, 48, 1-3.
PDB code: 3exb
16550276 H.Bayraktar, P.S.Ghosh, V.M.Rotello, and M.J.Knapp (2006).
Disruption of protein-protein interactions using nanoparticles: inhibition of cytochrome c peroxidase.
  Chem Commun (Camb), (), 1390-1392.  
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.  
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.  
10956001 V.W.Leesch, J.Bujons, A.G.Mauk, and B.M.Hoffman (2000).
Cytochrome c peroxidase-cytochrome c complex: locating the second binding domain on cytochrome c peroxidase with site-directed mutagenesis.
  Biochemistry, 39, 10132-10139.  
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.  
10593892 I.F.Sevrioukova, J.T.Hazzard, G.Tollin, and T.L.Poulos (1999).
The FMN to heme electron transfer in cytochrome P450BM-3. Effect of chemical modification of cysteines engineered at the FMN-heme domain interaction site.
  J Biol Chem, 274, 36097-36106.  
10608874 V.A.Roberts, and M.E.Pique (1999).
Definition of the interaction domain for cytochrome c on cytochrome c oxidase. III. Prediction of the docked complex by a complete, systematic search.
  J Biol Chem, 274, 38051-38060.  
10606521 X.Wang, and G.J.Pielak (1999).
Equilibrium thermodynamics of a physiologically-relevant heme-protein complex.
  Biochemistry, 38, 16876-16881.  
10608872 Y.Zhen, C.W.Hoganson, G.T.Babcock, and S.Ferguson-Miller (1999).
Definition of the interaction domain for cytochrome c on cytochrome c oxidase. I. Biochemical, spectral, and kinetic characterization of surface mutants in subunit ii of Rhodobacter sphaeroides cytochrome aa(3).
  J Biol Chem, 274, 38032-38041.  
9667934 D.Beratan, and S.Skourtis (1998).
Electron transfer mechanisms.
  Curr Opin Chem Biol, 2, 235-243.  
9790675 G.M.Soriano, M.V.Ponamarev, R.A.Piskorowski, and W.A.Cramer (1998).
Identification of the basic residues of cytochrome f responsible for electrostatic docking interactions with plastocyanin in vitro: relevance to the electron transfer reaction in vivo.
  Biochemistry, 37, 15120-15128.  
9136887 S.F.Sukits, J.E.Erman, and J.D.Satterlee (1997).
Proton NMR assignments and magnetic axes orientations for wild-type yeast iso-1-ferricytochrome c free in solution and bound to cytochrome c peroxidase.
  Biochemistry, 36, 5251-5259.  
8961943 H.Mei, K.Wang, S.McKee, X.Wang, J.L.Waldner, G.J.Pielak, B.Durham, and F.Millett (1996).
Control of formation and dissociation of the high-affinity complex between cytochrome c and cytochrome c peroxidase by ionic strength and the low-affinity binding site.
  Biochemistry, 35, 15800-15806.  
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.  
8961942 M.A.Miller (1996).
A complete mechanism for steady-state oxidation of yeast cytochrome c by yeast cytochrome c peroxidase.
  Biochemistry, 35, 15791-15799.  
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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