2EWK

The T24V mutant of tetraheme cytochrome c3 from Desulfovibrio Vulgaris Miyazaki F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Strategic roles of axial histidines in structure formation and redox regulation of tetraheme cytochrome c3.

Takayama, Y.Werbeck, N.D.Komori, H.Morita, K.Ozawa, K.Higuchi, Y.Akutsu, H.

(2008) Biochemistry 47: 9405-9415

  • DOI: 10.1021/bi8005708
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tetraheme cytochrome c 3 (cyt c 3) exhibits extremely low reduction potentials and unique properties. Since axial ligands should be the most important factors for this protein, every axial histidine of Desulfovibrio vulgaris Miyazaki F cyt c 3 was re ...

    Tetraheme cytochrome c 3 (cyt c 3) exhibits extremely low reduction potentials and unique properties. Since axial ligands should be the most important factors for this protein, every axial histidine of Desulfovibrio vulgaris Miyazaki F cyt c 3 was replaced with methionine, one by one. On mutation at the fifth ligand, the relevant heme could not be linked to the polypeptide, revealing the essential role of the fifth histidine in heme linking. The fifth histidine is the key residue in the structure formation and redox regulation of a c-type cytochrome. A crystal structure has been obtained for only H25M cyt c 3. The overall structure was not affected by the mutation except for the sixth methionine coordination at heme 3. NMR spectra revealed that each mutated methionine is coordinated to the sixth site of the relevant heme in the reduced state, while ligand conversion takes place at hemes 1 and 4 during oxidation at pH 7. The replacement of the sixth ligand with methionine caused an increase in the reduction potential of the mutated heme of 222-244 mV. The midpoint potential of a triheme H52M cyt c 3 is higher than that of the wild type by approximately 50 mV, suggesting a contribution of the tetraheme architecture to the lowering of the reduction potentials. The hydrogen bonding of Thr24 with an axial ligand induces a decrease in reduction potential of approximately 50 mV. In conclusion, the bis-histidine coordination is strategically essential for the structure formation and the extremely low reduction potential of cyt c 3.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c3
A
107Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 1 
Find proteins for P00132 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P00132
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.110 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.425α = 90.00
b = 67.537β = 90.00
c = 34.412γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SHELXmodel building
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance