2V08

Structure of wild-type Phormidium laminosum cytochrome c6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1021/ja072346g
  • Primary Citation of Related Structures:  
    2V07, 2V08

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C6
A, B
86Phormidium laminosumMutation(s): 0 
UniProt
Find proteins for F2Z292 (Phormidium laminosum)
Explore F2Z292 
Go to UniProtKB:  F2Z292
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z292
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
O [auth B],
P [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
Query on ZN

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.364α = 90
b = 57.364β = 90
c = 89.553γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description