1KF6

E. coli Quinol-Fumarate Reductase with Bound Inhibitor HQNO

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 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:  
    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-active molecule menaquinol (MQH(2)) transfers electrons to QFR by binding directly to the membrane-spanning region ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FUMARATE REDUCTASE FLAVOPROTEINA, E [auth M]602Escherichia coliMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00363 (Escherichia coli (strain K12))
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Go to UniProtKB:  P00363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FUMARATE REDUCTASE IRON-SULFUR PROTEINB, F [auth N]243Escherichia coliMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0AC47 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FUMARATE REDUCTASE 15 KDA HYDROPHOBIC PROTEINC, G [auth O]130Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A8Q0 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
FUMARATE REDUCTASE 13 KDA HYDROPHOBIC PROTEIND, H [auth P]119Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A8Q3 (Escherichia coli (strain K12))
Explore P0A8Q3 
Go to UniProtKB:  P0A8Q3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD
Download Ideal Coordinates CCD File 
 L [auth A], U [auth M]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
CE1 (Subject of Investigation/LOI)
Query on CE1
Download Ideal Coordinates CCD File 
 AA [auth O], BA [auth O], CA [auth O], DA [auth P], EA [auth P]O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
 Q [auth B], Y [auth N]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F3S
Query on F3S
Download Ideal Coordinates CCD File 
 P [auth B], X [auth N]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
HQO (Subject of Investigation/LOI)
Query on HQO
Download Ideal Coordinates CCD File 
 R [auth C], Z [auth N]2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
C16 H21 N O2
NZPACTGCRWDXCJ-UHFFFAOYSA-N		 Ligand Interaction
1PE
Query on 1PE
Download Ideal Coordinates CCD File 
 M [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
 O [auth B], W [auth N]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
OAA
Query on OAA
Download Ideal Coordinates CCD File 
 J [auth A], T [auth M]OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
 K [auth A], N [auth B], V [auth N]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
 I [auth A], S [auth M]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HQO PDBBind:  1KF6 Ki: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 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
b = 137.836β = 90
c = 273.451γ = 90
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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