1L0V

Quinol-Fumarate Reductase with Menaquinol Molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site.

Iverson, T.M.Luna-Chavez, C.Croal, L.R.Cecchini, G.Rees, D.C.

(2002) J Biol Chem 277: 16124-16130

  • DOI: 10.1074/jbc.M200815200
  • Primary Citation of Related Structures:  
    1KF6, 1KFY, 1L0V

  • PubMed Abstract: 
  • The quinol-fumarate reductase (QFR) respiratory complex of Escherichia coli is a four-subunit integral-membrane complex that catalyzes the final step of anaerobic respiration when fumarate is the terminal electron acceptor. The membrane-soluble redox ...

    The quinol-fumarate reductase (QFR) respiratory complex of Escherichia coli is a four-subunit integral-membrane complex that catalyzes the final step of anaerobic respiration when fumarate is the terminal electron acceptor. The membrane-soluble redox-active molecule menaquinol (MQH(2)) transfers electrons to QFR by binding directly to the membrane-spanning region. The crystal structure of QFR contains two quinone species, presumably MQH(2), bound to the transmembrane-spanning region. The binding sites for the two quinone molecules are termed Q(P) and Q(D), indicating their positions proximal (Q(P)) or distal (Q(D)) to the site of fumarate reduction in the hydrophilic flavoprotein and iron-sulfur protein subunits. It has not been established whether both of these sites are mechanistically significant. Co-crystallization studies of the E. coli QFR with the known quinol-binding site inhibitors 2-heptyl-4-hydroxyquinoline-N-oxide and 2-[1-(p-chlorophenyl)ethyl] 4,6-dinitrophenol establish that both inhibitors block the binding of MQH(2) at the Q(P) site. In the structures with the inhibitor bound at Q(P), no density is observed at Q(D), which suggests that the occupancy of this site can vary and argues against a structurally obligatory role for quinol binding to Q(D). A comparison of the Q(P) site of the E. coli enzyme with quinone-binding sites in other respiratory enzymes shows that an acidic residue is structurally conserved. This acidic residue, Glu-C29, in the E. coli enzyme may act as a proton shuttle from the quinol during enzyme turnover.


    Related Citations: 
    • Structure of the E. coli Fumarate Reductase Respiratory Complex
      Iverson, T.M., Luna-Chavez, C., Cecchini, G., Rees, D.C.
      (1999) Science 284: 1961
    • Overexpression, Purification, and Crystallization of the Membrane-Bound Fumarate Reductase from Eschericia coli
      Luna-Chavez, C., Iverson, T.M., Rees, D.C., Cecchini, G.
      (2000) Protein Expr Purif 19: 188

    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase flavoprotein subunitAM602Escherichia coliMutation(s): 0 
Gene Names: frdA
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Native Fumarate Reductase Complex
Find proteins for P00363 (Escherichia coli (strain K12))
Explore P00363 
Go to UniProtKB:  P00363
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase iron-sulfur proteinBN243Escherichia coliMutation(s): 0 
Gene Names: frdB
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Native Fumarate Reductase Complex
Find proteins for P0AC47 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AC47
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase 15 kDa hydrophobic proteinCO130Escherichia coliMutation(s): 0 
Gene Names: frdC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Native Fumarate Reductase Complex
Find proteins for P0A8Q0 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8Q0
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase 13 kDa hydrophobic proteinDP119Escherichia coliMutation(s): 0 
Gene Names: frdD
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Native Fumarate Reductase Complex
Find proteins for P0A8Q3 (Escherichia coli (strain K12))
Explore P0A8Q3 
Go to UniProtKB:  P0A8Q3
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, M
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MQ7
Query on MQ7

Download CCD File 
B, D, N, P
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
CE1
Query on CE1

Download CCD File 
D, O
O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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B, N
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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B, N
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

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B, N
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
OAA
Query on OAA

Download CCD File 
A, M
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.59α = 90
b = 138.09β = 90
c = 275.25γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance