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PDBsum entry 1ofw

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protein ligands Protein-protein interface(s) links
Electron transport PDB id
1ofw
Jmol
Contents
Protein chains
293 a.a. *
Ligands
HEC ×18
GOL ×4
ACT
Waters ×641
* Residue conservation analysis
PDB id:
1ofw
Name: Electron transport
Title: Three dimensional structure of the oxidized form of nine heme cytochromE C at ph 7.5
Structure: Nine-heme cytochromE C. Chain: a, b. Synonym: 9hcc
Source: Desulfovibrio desulfuricans. Organism_taxid: 876. Atcc: 27774
Biol. unit: Monomer (from PDB file)
Resolution:
1.5Å     R-factor:   0.171     R-free:   0.207
Authors: I.Bento,V.H.Teixeira,A.M.Baptista,C.M.Soares,P.M.Matias, M.A.Carrondo
Key ref:
I.Bento et al. (2003). Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies. J Biol Chem, 278, 36455-36469. PubMed id: 12750363 DOI: 10.1074/jbc.M301745200
Date:
22-Apr-03     Release date:   18-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9RN68  (CYC9_DESDA) -  Nine-heme cytochrome c
Seq:
Struc:
326 a.a.
293 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     3 terms  

 

 
DOI no: 10.1074/jbc.M301745200 J Biol Chem 278:36455-36469 (2003)
PubMed id: 12750363  
 
 
Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies.
I.Bento, V.H.Teixeira, A.M.Baptista, C.M.Soares, P.M.Matias, M.A.Carrondo.
 
  ABSTRACT  
 
The nine-heme cytochrome c is a monomeric multiheme cytochrome found in Desulfovibrio desulfuricans ATCC 27774. The polypeptide chain comprises 296 residues and wraps around nine hemes of type c. It is believed to take part in the periplasmic assembly of proteins involved in the mechanism of hydrogen cycling, receiving electrons from the tetraheme cytochrome c3. With the purpose of understanding the molecular basis of electron transfer processes in this cytochrome, we have determined the crystal structures of its oxidized and reduced forms at pH 7.5 and performed theoretical calculations of the binding equilibrium of protons and electrons in these structures. This integrated study allowed us to observe that the reduction process induced relevant conformational changes in several residues, as well as protonation changes in some protonatable residues. In particular, the surroundings of hemes I and IV constitute two areas of special interest. In addition, we were able to ascertain the groups involved in the redox-Bohr effect present in this cytochrome and the conformational changes that may underlie the redox-cooperativity effects on different hemes. Furthermore, the thermodynamic simulations provide evidence that the N- and C-terminal domains function in an independent manner, with the hemes belonging to the N-terminal domain showing, in general, a lower redox potential than those found in the C-terminal domain. In this way, electrons captured by the N-terminal domain could easily flow to the C-terminal domain, allowing the former to capture more electrons. A notable exception is heme IX, which has low redox potential and could serve as the exit path for electrons toward other proteins in the electron transfer pathway.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Detailed view of heme I and its surroundings. a, oxidized form at pH 5.5. b, oxidized form at pH 7.5. c, reduced form at pH 7.5. Carbon atoms are shown in yellow, oxygen atoms in red, nitrogen atoms in blue, and the iron atom in magenta; the H-bond distances are represented as dashed red lines. Prepared with PyMOL (77). Haem, heme; Prop, propionate.
Figure 5.
FIG. 5. Detailed view of heme IV and its surroundings. a, oxidized form at pH 5.5. b, oxidized form at pH 7.5. c, reduced form at pH 7.5. Carbon atoms are shown in yellow, oxygen atoms in red, nitrogen atoms in blue, and the iron atom in magenta; the H-bond distances are represented as dashed red lines. Prepared with PyMOL (77). Haem, heme; Prop, propionate.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 36455-36469) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19423328 S.El Ichi, M.N.Marzouki, and H.Korri-Youssoufi (2009).
Direct monitoring of pollutants based on an electrochemical biosensor with novel peroxidase (POX1B).
  Biosens Bioelectron, 24, 3084-3090.  
18205609 I.I.Pottosin, C.S.Chamorovsky, and S.K.Chamorovsky (2007).
Cooperative interaction of high-potential hemes in the cytochrome subunit of the photosynthetic reaction center of bacterium Ectothiorhodospira shaposhnikovii.
  Biochemistry (Mosc), 72, 1254-1260.  
16341896 R.E.Di Paolo, P.M.Pereira, I.Gomes, F.M.Valente, I.A.Pereira, and R.Franco (2006).
Resonance Raman fingerprinting of multiheme cytochromes from the cytochrome c3 family.
  J Biol Inorg Chem, 11, 217-224.  
16169983 A.S.Oliveira, V.H.Teixeira, A.M.Baptista, and C.M.Soares (2005).
Reorganization and conformational changes in the reduction of tetraheme cytochromes.
  Biophys J, 89, 3919-3930.  
16234915 C.G.Mowat, and S.K.Chapman (2005).
Multi-heme cytochromes--new structures, new chemistry.
  Dalton Trans, (), 3381-3389.  
15764652 L.Rivas, C.M.Soares, A.M.Baptista, J.Simaan, R.E.Di Paolo, D.H.Murgida, and P.Hildebrandt (2005).
Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies.
  Biophys J, 88, 4188-4199.  
15111396 V.H.Teixeira, A.M.Baptista, and C.M.Soares (2004).
Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3).
  Biophys J, 86, 2773-2785.  
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.

 

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