2BS2

QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Evidence for Transmembrane Proton Transfer in a Dihaem-Containing Membrane Protein Complex.

Madej, M.G.Nasiri, H.R.Hilgendorff, N.S.Schwalbe, H.Lancaster, C.R.D.

(2006) EMBO J 25: 4963

  • DOI: 10.1038/sj.emboj.7601361
  • Primary Citation of Related Structures:  
    2BS2

  • PubMed Abstract: 
  • Membrane protein complexes can support both the generation and utilisation of a transmembrane electrochemical proton potential ('proton-motive force'), either by transmembrane electron transfer coupled to protolytic reactions on opposite sides of the membrane or by transmembrane proton transfer ...

    Membrane protein complexes can support both the generation and utilisation of a transmembrane electrochemical proton potential ('proton-motive force'), either by transmembrane electron transfer coupled to protolytic reactions on opposite sides of the membrane or by transmembrane proton transfer. Here we provide the first evidence that both of these mechanisms are combined in the case of a specific respiratory membrane protein complex, the dihaem-containing quinol:fumarate reductase (QFR) of Wolinella succinogenes, so as to facilitate transmembrane electron transfer by transmembrane proton transfer. We also demonstrate the non-functionality of this novel transmembrane proton transfer pathway ('E-pathway') in a variant QFR where a key glutamate residue has been replaced. The 'E-pathway', discussed on the basis of the 1.78-Angstrom-resolution crystal structure of QFR, can be concluded to be essential also for the viability of pathogenic epsilon-proteobacteria such as Helicobacter pylori and is possibly relevant to proton transfer in other dihaem-containing membrane proteins, performing very different physiological functions.


    Related Citations: 
    • Wolinella Succinogenes Quinol:Fumarate Reductase -2.2 Angstrom Resolution Crystal Structure and the E-Pathway Hypothesis of Coupled Transmembrane Proton and Electron Transfer
      Lancaster, C.R.D.
      (2002) Biochim Biophys Acta 1565: 215
    • A Third Crystal Form of Wolinella Succinogenes Quinol:Fumarate Reductase Reveals Domain Closure at the Site of Fumarate Reduction
      Lancaster, C.R.D., Gross, R., Simon, J.
      (2001) Eur J Biochem 268: 1820
    • Essential Role of Glu-C66 for Menaquinol Oxidation Indicates Transmembrane Electrochemical Potential Generation by Wolinella Succinogenes Fumarate Reductase
      Lancaster, C.R.D., Gross, R., Haas, A., Ritter, M., Maentele, W., Simon, J., Kroeger, A.
      (2000) Proc Natl Acad Sci U S A 97: 13051
    • Structure of Fumarate Reductase from Wolinella Succinogenes at 2.2 Angstroms Resolution
      Lancaster, C.R.D., Kroeger, A., Auer, M., Michel, H.
      (1999) Nature 402: 377

    Organizational Affiliation

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOL-FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT AA, D660Wolinella succinogenesMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P17412 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17412 
Go to UniProtKB:  P17412
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17412
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOL-FUMARATE REDUCTASE IRON-SULFUR SUBUNIT BB, E241Wolinella succinogenesMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P17596 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17596 
Go to UniProtKB:  P17596
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17596
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOL-FUMARATE REDUCTASE DIHEME CYTOCHROME B SUBUNIT CC, F256Wolinella succinogenesMutation(s): 0 
EC: 1.3.99.1
Membrane Entity: Yes 
UniProt
Find proteins for P17413 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17413 
Go to UniProtKB:  P17413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17413
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A],
P [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HEM
Query on HEM

Download Ideal Coordinates CCD File 
M [auth C],
N [auth C],
V [auth F],
W [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
LMT
Query on LMT

Download Ideal Coordinates CCD File 
O [auth C],
X [auth F]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
L [auth B],
U [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
K [auth B],
T [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
J [auth B],
S [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FUM
Query on FUM

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth D]
FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
R [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.104α = 90
b = 188.766β = 104.47
c = 117.817γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-25
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance