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PDBsum entry 2b10
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protein ligands Protein-protein interface(s) links
Oxidoreductase/electron transport PDB id
2b10

 

 

 

 

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Contents
Protein chains
294 a.a. *
108 a.a. *
Ligands
ZNH ×2
HEM ×2
Waters ×23
* Residue conservation analysis
PDB id:
2b10
Name: Oxidoreductase/electron transport
Title: Crystal structure of the protein-protein complex between f82s cytochromE C and cytochromE C peroxidase
Structure: CytochromE C peroxidase, mitochondrial. Chain: a, c. Synonym: ccp. Engineered: yes. CytochromE C iso-1. Chain: b, d. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ccp1, ccp, cpo. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: cyc1. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.80Å     R-factor:   0.285     R-free:   0.306
Authors: S.A.Kang,B.R.Crane
Key ref:
S.A.Kang and B.R.Crane (2005). Effects of interface mutations on association modes and electron-transfer rates between proteins. Proc Natl Acad Sci U S A, 102, 15465-15470. PubMed id: 16227441 DOI: 10.1073/pnas.0505176102
Date:
15-Sep-05     Release date:   25-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		361 a.a.
294 a.a.
Protein chains
Pfam   ArchSchema ?
P00044  (CYC1_YEAST) -  Cytochrome c isoform 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		109 a.a.
108 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: Chains A, C: 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 = ZNH) matches with 95.45% similarity
   Enzyme class 3: Chains B, D: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.0505176102 Proc Natl Acad Sci U S A 102:15465-15470 (2005)
PubMed id: 16227441  
 
 
Effects of interface mutations on association modes and electron-transfer rates between proteins.
S.A.Kang, B.R.Crane.
 
  ABSTRACT  
 
Although bonding networks determine electron-transfer (ET) rates within proteins, the mechanism by which structure and dynamics influence ET across protein interfaces is not well understood. Measurements of photochemically induced ET and subsequent charge recombination between Zn-porphyrin-substituted cytochrome c peroxidase and cytochrome c in single crystals correlate reactivity with defined structures for different association modes of the redox partners. Structures and ET rates in crystals are consistent with tryptophan oxidation mediating charge recombination reactions. Conservative mutations at the interface can drastically affect how the proteins orient and dispose redox centers. Whereas some configurations are ET inactive, the wild-type complex exhibits the fastest recombination rate. Other association modes generate ET rates that do not correlate with predictions based on cofactor separations or simple bonding pathways. Inhibition of photoinduced ET at <273 K indicates gating by small-amplitude dynamics, even within the crystal. Thus, different associations achieve states of similar reactivity, and within those states conformational fluctuations enable interprotein ET.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Reactions initiated by photoinduced ET between ZnCcP and Fe(III) yCc. 		Figure 2.
Fig. 2. Complexes of ZnCcP with various Cc mutants have different association modes. (A) Representative ribbon diagrams for ZnCcP bound to Cc variants. From left to right: yCc WT, F82W, and F82S mutants; yCc F82Y and F82I mutants; horse Cc; yCc K72S/F82Y. (B) Relative positioning and interface structures for the ZnCcP:F82W yCc (Left) and ZnCcP:yCc F82I (Right) complexes. Cc (gray ribbons, top) rotates 90° and translates8Åinthe F82I mutant generating altered heme orientations (yellow bonds), interprotein contacts (black and orange side chains), and intervening solvent structure (red spheres) with CcP (yellow, below) compared with the F82W complex. (C) Superposition of ZnCcP from the two ZnCcP: F82S yCc complexes (red and blue) indicate variability in Cc positioning within the asymmetric unit.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21469225 A.M.Blanco-Rodríguez, A.J.Di Bilio, C.Shih, A.K.Museth, I.P.Clark, M.Towrie, A.Cannizzo, J.Sudhamsu, B.R.Crane, J.Sýkora, J.R.Winkler, H.B.Gray, S.Záliš, and A.Vlček (2011).
Phototriggering electron flow through Re(I)-modified Pseudomonas aeruginosa azurins.
  Chemistry, 17, 5350-5361.  
21458342 J.Karanicolas, J.E.Corn, I.Chen, L.A.Joachimiak, O.Dym, S.H.Peck, S.Albeck, T.Unger, W.Hu, G.Liu, S.Delbecq, G.T.Montelione, C.P.Spiegel, D.R.Liu, and D.Baker (2011).
A de novo protein binding pair by computational design and directed evolution.
  Mol Cell, 42, 250-260.
PDB codes: 3q9n 3q9u 3qa9
20376873 H.K.Ly, M.A.Marti, D.F.Martin, D.Alvarez-Paggi, W.Meister, A.Kranich, I.M.Weidinger, P.Hildebrandt, and D.H.Murgida (2010).
Thermal fluctuations determine the electron-transfer rates of cytochrome c in electrostatic and covalent complexes.
  Chemphyschem, 11, 1225-1235.  
19243185 A.M.Carver, M.De, H.Bayraktar, S.Rana, V.M.Rotello, and M.J.Knapp (2009).
Intermolecular electron-transfer catalyzed on nanoparticle surfaces.
  J Am Chem Soc, 131, 3798-3799.  
18717535 A.D.Patel, J.M.Nocek, and B.M.Hoffman (2008).
Kinetic-dynamic model for conformational control of an electron transfer photocycle: mixed-metal hemoglobin hybrids.
  J Phys Chem B, 112, 11827-11837.  
18728193 Y.C.Kim, C.Tang, G.M.Clore, and G.Hummer (2008).
Replica exchange simulations of transient encounter complexes in protein-protein association.
  Proc Natl Acad Sci U S A, 105, 12855-12860.  
18083189 Y.C.Kim, and G.Hummer (2008).
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.
  J Mol Biol, 375, 1416-1433.  
17517617 M.M.Haque, K.Panda, J.Tejero, K.S.Aulak, M.A.Fadlalla, A.T.Mustovich, and D.J.Stuehr (2007).
A connecting hinge represses the activity of endothelial nitric oxide synthase.
  Proc Natl Acad Sci U S A, 104, 9254-9259.  
17146057 A.N.Volkov, J.A.Worrall, E.Holtzmann, and M.Ubbink (2006).
Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR.
  Proc Natl Acad Sci U S A, 103, 18945-18950.
PDB code: 2gb8
16605268 N.A.Belikova, Y.A.Vladimirov, A.N.Osipov, A.A.Kapralov, V.A.Tyurin, M.V.Potapovich, L.V.Basova, J.Peterson, I.V.Kurnikov, and V.E.Kagan (2006).
Peroxidase activity and structural transitions of cytochrome c bound to cardiolipin-containing membranes.
  Biochemistry, 45, 4998-5009.  
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.

 

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