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PDBsum entry 2wdr

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2wdr
Jmol
Contents
Protein chains
588 a.a. *
238 a.a. *
122 a.a. *
105 a.a. *
Ligands
FAD ×3
TEO ×3
FES ×3
SF4 ×3
F3S ×3
HEM ×3
PCI ×3
Metals
_NA ×3
* Residue conservation analysis
PDB id:
2wdr
Name: Oxidoreductase
Title: E. Coli succinate:quinone oxidoreductase (sqr) with pentachlorophenol bound
Structure: Succinate dehydrogenase flavoprotein subunit. Chain: a, e, i. Engineered: yes. Other_details: fad atom c8m is covalently linked to ne2 of his45. Succinate dehydrogenase iron-sulfur subunit. Chain: b, f, j. Engineered: yes. Succinate dehydrogenase cytochrome b556 subunit.
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.20Å     R-factor:   0.199     R-free:   0.228
Authors: J.Ruprecht,V.Yankovskaya,E.Maklashina,S.Iwata,G.Cecchini
Key ref:
J.Ruprecht et al. (2009). Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. J Biol Chem, 284, 29836-29846. PubMed id: 19710024 DOI: 10.1074/jbc.M109.010058
Date:
25-Mar-09     Release date:   25-Aug-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AC41  (DHSA_ECOLI) -  Succinate dehydrogenase flavoprotein subunit
Seq:
Struc:
 
Seq:
Struc:
588 a.a.
588 a.a.
Protein chains
Pfam   ArchSchema ?
P07014  (DHSB_ECOLI) -  Succinate dehydrogenase iron-sulfur subunit
Seq:
Struc:
238 a.a.
238 a.a.
Protein chains
Pfam   ArchSchema ?
P69054  (DHSC_ECOLI) -  Succinate dehydrogenase cytochrome b556 subunit
Seq:
Struc:
129 a.a.
122 a.a.
Protein chains
Pfam   ArchSchema ?
P0AC44  (DHSD_ECOLI) -  Succinate dehydrogenase hydrophobic membrane anchor subunit
Seq:
Struc:
115 a.a.
105 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, E, F, I, J: E.C.1.3.5.1  - Succinate dehydrogenase (quinone).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: Succinate + a quinone = fumarate + a quinol
Succinate
Bound ligand (Het Group name = TEO)
matches with 88.89% similarity
+ quinone
= fumarate
+ quinol
      Cofactor: FAD; Iron-sulfur
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     electron carrier activity     14 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M109.010058 J Biol Chem 284:29836-29846 (2009)
PubMed id: 19710024  
 
 
Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini.
 
  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.
 
  Selected figure(s)  
 
Figure 2.
Architecture of the dicarboxylate-binding site and ligand in the carboxin-inhibited structure. The stereo figure shows residues within 4.0 Å of the ligand TEO, a malate-like intermediate. Interactions between residues and the ligand are shown as red dotted lines. The density, shown as a blue mesh, is a 2mF[o] − DF[c] map, contoured at 1.8 σ. Residues 251–253 and 354 of SdhA have been removed to enable a clearer view of the binding site.
Figure 3.
An unusual cis-peptide bond between Val-A392 and Ser-A393. The stereo figure shows residues around the cis-peptide (labeled cP). Polar contacts between residues are shown as red dotted lines, water molecules as cyan spheres, and a metal ion as a gray sphere. The density, shown as a blue mesh, is a 2mF[o] − DF[c] map, contoured at 1.3 σ.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 29836-29846) copyright 2009.  
  Figures were selected by an automated process.