2V07

Structure of the Arabidopsis thaliana cytochrome c6A V52Q variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Modulation of heme redox potential in the cytochrome c6 family.

Worrall, J.A.Schlarb-Ridley, B.G.Reda, T.Marcaida, M.J.Moorlen, R.J.Wastl, J.Hirst, J.Bendall, D.S.Luisi, B.F.Howe, C.J.

(2007) J. Am. Chem. Soc. 129: 9468-9475

  • DOI: 10.1021/ja072346g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome c6A is a unique dithio-cytochrome of green algae and plants. It has a very similar core structure to that of bacterial and algal cytochromes c6 but is unable to fulfill the same function of transferring electrons from cytochrome f to photo ...

    Cytochrome c6A is a unique dithio-cytochrome of green algae and plants. It has a very similar core structure to that of bacterial and algal cytochromes c6 but is unable to fulfill the same function of transferring electrons from cytochrome f to photosystem I. A key feature is that its heme midpoint potential is more than 200 mV below that of cytochrome c6 despite having His and Met as axial heme-iron ligands. To identify the molecular origins of the difference in potential, the structure of cytochrome c6 from the cyanobacterium Phormidium laminosum has been determined by X-ray crystallography and compared with the known structure of cytochrome c6A. One salient difference of the heme pockets is that a highly conserved Gln (Q51) in cytochrome c6 is replaced by Val (V52) in c6A. Using protein film voltammetry, we found that swapping these residues raised the c6A potential by +109 mV and decreased that of c6 by almost the same extent, -100 mV. X-ray crystallography of the V52Q protein showed that the Gln residue adopts the same configuration relative to the heme as in cytochrome c6 and we propose that this stereochemistry destabilizes the oxidized form of the heme. Consequently, replacement of Gln by Val was probably a key step in the evolution of cytochrome c6A from cytochrome c6, inhibiting reduction by the cytochrome b6f complex and facilitating establishment of a new function.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge, UK. jw510@mole.bio.cam.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C6
A
105Arabidopsis thalianaMutation(s): 2 
Gene Names: PETJ
Find proteins for Q93VA3 (Arabidopsis thaliana)
Go to UniProtKB:  Q93VA3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.783α = 90.00
b = 57.783β = 90.00
c = 65.145γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2019-01-23
    Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary