2WDV

E. coli succinate:quinone oxidoreductase (SQR) with an empty quinone- binding pocket

• PDB DOI: https://doi.org/10.2210/pdb2WDV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2009-03-26 Released: 2009-08-25 
• Deposition Author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.233 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Literature

Structure of Escherichia Coli Succinate:Quinone Oxidoreductase with an Occupied and Empty Quinone- Binding Site.

Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

(2009) J Biol Chem 284: 29836

• PubMed: 19710024 
• DOI: https://doi.org/10.1074/jbc.M109.010058
• Primary Citation of Related Structures:  
  2WDQ, 2WDR, 2WDV


• PubMed Abstract: 
  

  Three new structures of Escherichia coli succinate-quinone oxidoreductase (SQR) have been solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present has been solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site. The other new structures are with the Q-site inhibitor pentachlorophenol and with an empty Q-site. These structures reveal important details unresolved in earlier structures. Comparison of the new SQR structures shows how subtle rearrangements of the quinone-binding site accommodate the different inhibitors. The position of conserved water molecules near the quinone binding pocket leads to a reassessment of possible water-mediated proton uptake networks that complete reduction of ubiquinone. The dicarboxylate-binding site in the soluble domain of SQR is highly similar to that seen in high resolution structures of avian SQR (PDB 2H88) and soluble flavocytochrome c (PDB 1QJD) showing mechanistically significant structural features conserved across prokaryotic and eukaryotic SQRs.

---

Organizational Affiliation: 

Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW72AZ, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 362.61 kDa 
• Atom Count: 24,855 
• Modelled Residue Count: 3,156 
• Deposited Residue Count: 3,210 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT	A, E, I	588	Escherichia coli	Mutation(s): 0  EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12)) Explore P0AC41  Go to UniProtKB:  P0AC41

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT	B, F, J	238	Escherichia coli	Mutation(s): 0  EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P07014 (Escherichia coli (strain K12)) Explore P07014  Go to UniProtKB:  P07014

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT	C, G, K	129	Escherichia coli	Mutation(s): 0  EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P69054 (Escherichia coli (strain K12)) Explore P69054  Go to UniProtKB:  P69054

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN	D, H, L	115	Escherichia coli	Mutation(s): 0  EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12)) Explore P0AC44  Go to UniProtKB:  P0AC44

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	AA [auth I], M [auth A], T [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM	GA [auth K], S [auth C], Z [auth G]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SF4	EA [auth J], Q [auth B], X [auth F]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	FA [auth J], R [auth B], Y [auth F]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES	DA [auth J], P [auth B], W [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
TEO	BA [auth I], N [auth A], U [auth E]	MALATE LIKE INTERMEDIATE C4 H4 O5 QFBHYOKSQPPXHZ-UWTATZPHSA-L
NA	CA [auth I], O [auth A], V [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.233 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.34	α = 90
b = 184.847	β = 90
c = 204.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary