2ACZ

Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction.

Horsefield, R.Yankovskaya, V.Sexton, G.Whittingham, W.Shiomi, K.Omura, S.Byrne, B.Cecchini, G.Iwata, S.

(2006) J.Biol.Chem. 281: 7309-7316

  • DOI: 10.1074/jbc.M508173200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The transfer of electrons and protons between membrane-bound respiratory complexes is facilitated by lipid-soluble redox-active quinone molecules (Q). This work presents a structural analysis of the quinone-binding site (Q-site) identified in succina ...

    The transfer of electrons and protons between membrane-bound respiratory complexes is facilitated by lipid-soluble redox-active quinone molecules (Q). This work presents a structural analysis of the quinone-binding site (Q-site) identified in succinate:ubiquinone oxidoreductase (SQR) from Escherichia coli. SQR, often referred to as Complex II or succinate dehydrogenase, is a functional member of the Krebs cycle and the aerobic respiratory chain and couples the oxidation of succinate to fumarate with the reduction of quinone to quinol (QH(2)). The interaction between ubiquinone and the Q-site of the protein appears to be mediated solely by hydrogen bonding between the O1 carbonyl group of the quinone and the side chain of a conserved tyrosine residue. In this work, SQR was co-crystallized with the ubiquinone binding-site inhibitor Atpenin A5 (AA5) to confirm the binding position of the inhibitor and reveal additional structural details of the Q-site. The electron density for AA5 was located within the same hydrophobic pocket as ubiquinone at, however, a different position within the pocket. AA5 was bound deeper into the site prompting further assessment using protein-ligand docking experiments in silico. The initial interpretation of the Q-site was re-evaluated in the light of the new SQR-AA5 structure and protein-ligand docking data. Two binding positions, the Q(1)-site and Q(2)-site, are proposed for the E. coli SQR quinone-binding site to explain these data. At the Q(2)-site, the side chains of a serine and histidine residue are suitably positioned to provide hydrogen bonding partners to the O4 carbonyl and methoxy groups of ubiquinone, respectively. This allows us to propose a mechanism for the reduction of ubiquinone during the catalytic turnover of the enzyme.


    Organizational Affiliation

    Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase flavoprotein subunit
A
588Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sdhA
EC: 1.3.5.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P0AC41 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC41
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase iron-sulfur protein
B
238Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sdhB
EC: 1.3.5.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P07014 (Escherichia coli (strain K12))
Go to UniProtKB:  P07014
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome b556 subunit
C
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sdhC (cybA)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P69054 (Escherichia coli (strain K12))
Go to UniProtKB:  P69054
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase hydrophobic membrane anchor protein
D
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sdhD
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P0AC44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC44
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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Download CCD File 
B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
AT5
Query on AT5

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Download CCD File 
C
3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE
ATPENIN A5; AA5
C15 H21 Cl2 N O5
OVULNOOPECCZRG-CIUDSAMLSA-N
 Ligand Interaction
CDN
Query on CDN

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Download CCD File 
C
CARDIOLIPIN
C58 H120 O17 P2
GKRASOJOCMJQMF-DUXRJKJQSA-N
 Ligand Interaction
FES
Query on FES

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

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A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
HEB
Query on HEB

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Download CCD File 
C
HEME B/C
HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-ICENSXKYDL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.264 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 138.759α = 90.00
b = 138.759β = 90.00
c = 521.873γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance