1OFY

three dimensional structure of the reduced form of nine-heme cytochrome c at ph 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Redox-Bohr and Other Cooperativity Effects in the Nine-Heme Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies

Bento, I.Teixeira, V.H.Baptista, A.M.Soares, C.M.Matias, P.M.Carrondo, M.A.

(2003) J.Biol.Chem. 278: 36455

  • DOI: 10.1074/jbc.M301745200
  • Primary Citation of Related Structures:  1OFW

  • PubMed 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 assembl ...

    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.


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NINE HEME CYTOCHROME C
A, B
296Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)N/A
Find proteins for Q9RN68 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949))
Go to UniProtKB:  Q9RN68
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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Download CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.275 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.400α = 90.00
b = 105.660β = 103.35
c = 80.940γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance