1KF6

E. coli Quinol-Fumarate Reductase with Bound Inhibitor HQNO

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.231 

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:  

  • 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 Escherichia coli Fumarate reductase respiratory complex
      Iverson, T.M.,Luna-Chavez, C.,Cecchini, G.,Rees, D.C.
      (1999) Science 284: 1961

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FUMARATE REDUCTASE FLAVOPROTEIN
A, M
602Escherichia coli (strain K12)Gene Names: frdA
EC: 1.3.5.4
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Fumarate Reductase Complex
Find proteins for P00363 (Escherichia coli (strain K12))
Go to UniProtKB:  P00363
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FUMARATE REDUCTASE IRON-SULFUR PROTEIN
B, N
243Escherichia coli (strain K12)Gene Names: frdB
EC: 1.3.5.1
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Fumarate Reductase Complex
Find proteins for P0AC47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FUMARATE REDUCTASE 15 KDA HYDROPHOBIC PROTEIN
C, O
130Escherichia coli (strain K12)Gene Names: frdC
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Fumarate Reductase Complex
Find proteins for P0A8Q0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8Q0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FUMARATE REDUCTASE 13 KDA HYDROPHOBIC PROTEIN
D, P
119Escherichia coli (strain K12)Gene Names: frdD
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Fumarate Reductase Complex
Find proteins for P0A8Q3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8Q3
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
A, M
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4
Download SDF File 
Download CCD File 
B, N
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CE1
Query on CE1
Download SDF File 
Download CCD File 
O, P
O-DODECANYL OCTAETHYLENE GLYCOL
THESIT
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
 Ligand Interaction
F3S
Query on F3S
Download SDF File 
Download CCD File 
B, N
2,4,6,7-tetrathia-1$l^{3},3$l^{2},5$l^{3}-triferrabicyclo[3.1.1]heptane
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT
Download SDF File 
Download CCD File 
A, B, N
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD
Download SDF File 
Download CCD File 
A, M
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES
Download SDF File 
Download CCD File 
B, N
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
OAA
Query on OAA
Download SDF File 
Download CCD File 
A, M
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
HQO
Query on HQO
Download SDF File 
Download CCD File 
C, N
2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
2-HEPTYL-1-OXY-QUINOLIN-4-OL
C16 H21 N O2
NZPACTGCRWDXCJ-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE
Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HQOKi: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.505α = 90.00
b = 137.836β = 90.00
c = 273.451γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
REFMACrefinement
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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