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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
FUMARATE REDUCTASE FLAVOPROTEINA,
E [auth M]
602Escherichia coliMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00363 (Escherichia coli (strain K12))
Explore P00363 
Go to UniProtKB:  P00363
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00363
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FUMARATE REDUCTASE IRON-SULFUR PROTEINB,
F [auth N]
243Escherichia coliMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0AC47 (Escherichia coli (strain K12))
Explore P0AC47 
Go to UniProtKB:  P0AC47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AC47
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence 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 Groups  
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UniProt GroupP0A8Q0
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8Q3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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L [auth A],
U [auth M]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CE1
Query on CE1

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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
SF4
Query on SF4

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Q [auth B],
Y [auth N]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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P [auth B],
X [auth N]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
HQO
Query on HQO

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R [auth C],
Z [auth N]
2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
C16 H21 N O2
NZPACTGCRWDXCJ-UHFFFAOYSA-N
1PE
Query on 1PE

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M [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
FES
Query on FES

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O [auth B],
W [auth N]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
OAA
Query on OAA

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J [auth A],
T [auth M]
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
ACT
Query on ACT

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K [auth A],
N [auth B],
V [auth N]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
K
Query on K

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I [auth A],
S [auth M]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
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
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description