2BS3

GLU C180 -> GLN VARIANT QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Experimental Support for the E-Pathway Hypothesis of Coupled Transmembrane Electron and Proton Transfer in Dihemic Quinol:Fumarate Reductase

Lancaster, C.R.D.Sauer, U.S.Gross, R.Haas, A.H.Graf, J.Schwalbe, H.Maentele, W.Simon, J.Madej, G.

(2005) Proc Natl Acad Sci U S A 102: 18860

  • DOI: 10.1073/pnas.0509711102
  • Primary Citation of Related Structures:  
    2BS3, 2BS4

  • PubMed Abstract: 
  • Reconciliation of apparently contradictory experimental results obtained on the quinol:fumarate reductase, a diheme-containing respiratory membrane protein complex from Wolinella succinogenes, was previously obtained by the proposal of the so-called "E pathway hypothesis ...

    Reconciliation of apparently contradictory experimental results obtained on the quinol:fumarate reductase, a diheme-containing respiratory membrane protein complex from Wolinella succinogenes, was previously obtained by the proposal of the so-called "E pathway hypothesis." According to this hypothesis, transmembrane electron transfer via the heme groups is strictly coupled to cotransfer of protons via a transiently established pathway thought to contain the side chain of residue Glu-C180 as the most prominent component. Here we demonstrate that, after replacement of Glu-C180 with Gln or Ile by site-directed mutagenesis, the resulting mutants are unable to grow on fumarate, and the membrane-bound variant enzymes lack quinol oxidation activity. Upon solubilization, however, the purified enzymes display approximately 1/10 of the specific quinol oxidation activity of the wild-type enzyme and unchanged quinol Michaelis constants, K(m). The refined x-ray crystal structures at 2.19 A and 2.76 A resolution, respectively, rule out major structural changes to account for these experimental observations. Changes in the oxidation-reduction heme midpoint potential allow the conclusion that deprotonation of Glu-C180 in the wild-type enzyme facilitates the reoxidation of the reduced high-potential heme. Comparison of solvent isotope effects indicates that a rate-limiting proton transfer step in the wild-type enzyme is lost in the Glu-C180 --> Gln variant. The results provide experimental evidence for the validity of the E pathway hypothesis and for a crucial functional role of Glu-C180.


    Related Citations: 
    • Wolinella Succinogenes Quinol:Fumarate Reductase and its Comparison to E. Coli Succinate:Quinone Reductase
      Lancaster, C.R.D.
      (2003) FEBS Lett 555: 21
    • 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, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany. roy.lancaster@mpibp-frankfurt.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOL-FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT AA, D656Wolinella 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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOL-FUMARATE REDUCTASE IRON-SULFUR SUBUNIT BB, E239Wolinella 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
CIT
Query on CIT

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 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
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: 2.19 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • 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

  • Deposited Date: 2005-05-14 
  • Released Date: 2005-12-13 
  • Deposition Author(s): Lancaster, C.R.D.

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance