PDBsum entry 2wdv

Oxidoreductase

PDB id: 2wdv

Contents

Protein chains

588 a.a.

238 a.a.

121 a.a.

105 a.a.

Ligands

FAD ×3

TEO ×3

FES ×3

SF4 ×3

F3S ×3

HEM ×3

Metals

_NA ×3

References listed in PDB file

Key reference

Title

Structure of escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-Binding site.

Authors

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

Ref.

J Biol Chem, 2009, 284, 29836-29846. [DOI no: 10.1074/jbc.M109.010058]

PubMed id

19710024

Note: In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above have been manually determined.

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.

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.