1AWP

RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The reduction potential of cytochrome b5 is modulated by its exposed heme edge.

Rivera, M., Seetharaman, R., Girdhar, D., Wirtz, M., Zhang, X., Wang, X., White, S.

(1998) Biochemistry 37: 1485-1494

  • DOI: 10.1021/bi972390g

  • PubMed Abstract: 

    • When the reduction potential of cytochrome b5 is measured with the aid of several different surface-modified electrodes that function on the basis of electrostatic interactions with the protein, the resultant values have been consistently more positi ...

    When the reduction potential of cytochrome b5 is measured with the aid of several different surface-modified electrodes that function on the basis of electrostatic interactions with the protein, the resultant values have been consistently more positive (40-100 mV) than the reduction potentials measured with potentiometric methods. In this paper, we report that the heme edge containing the exposed heme propionate, a heme methyl, and a heme vinyl, and which constitutes part of the surface of cytochrome b5, modulates its reduction potential. The positive shifts observed in the voltammetric measurements appear to originate from the formation of a complex between cytochrome b5 and the modified electrode surface which (a) neutralizes the charge on the heme propionate located on the exposed heme edge and (b) lowers the dielectric of the exposed heme microenvironment by excluding water from the complex interface, factors which result in the destabilization of the positive charge on the ferric heme with respect to the neutral ferrous heme. The observed positive shift, which is induced by complexation at the electrode surface, may indicate that similar shifts in the reduction potential of cytochrome b5 occur when it forms a complex with physiological partners, prior to electron transfer. The effect of the value of the dielectric constant on the reduction potential of cytochrome b5 was corroborated by preparing the V45L/V61L double mutant whose reduction potential was measured to be 50 mV more negative than the value measured for the wild type protein. The negative shift in the reduction potential of the mutant protein was explained by the increased accessibility of water to the heme binding site, as observed in its X-ray crystal structure.

    Organizational Affiliation: 

    Department of Chemistry, Oklahoma State University, Stillwater 74078-3071, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B5
A, B
92Rattus norvegicusMutation(s): 2 
Gene Names: Cyb5b (Cyb5m, Omb5)
Find proteins for P04166 (Rattus norvegicus)
Go to UniProtKB:  P04166
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download SDF File 
Download CCD File 
A, B
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: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.640α = 90.00
b = 71.190β = 90.00
c = 73.780γ = 90.00
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1997-10-03 
  • Released Date: 1998-10-28 
  • Deposition Author(s): Wang, X., Zhang, X.

Revision History 

  • Version 1.0: 1998-10-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance