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

* Residue conservation analysis

PDB id:

2wdv

Name:

Oxidoreductase

Title:

E. Coli succinate:quinone oxidoreductase (sqr) with an empty quinone- binding pocket

Structure:

Succinate dehydrogenase flavoprotein subunit. Chain: a, e, i. Engineered: yes. Other_details: fad atom c8m is covalently linked to ne2 of sdha 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: 0.206 R-free: 0.233

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:

26-Mar-09 Release date: 25-Aug-09

Protein chains

P0AC41  (SDHA_ECOLI) -  Succinate dehydrogenase flavoprotein subunit from Escherichia coli (strain K12)

Seq: 588 a.a.

Struc: 588 a.a.

Protein chains

P07014  (SDHB_ECOLI) -  Succinate dehydrogenase iron-sulfur subunit from Escherichia coli (strain K12)

Seq: 238 a.a.

Struc: 238 a.a.

Protein chains

P69054  (DHSC_ECOLI) -  Succinate dehydrogenase cytochrome b556 subunit from Escherichia coli (strain K12)

Seq: 129 a.a.

Struc: 121 a.a.

Protein chains

P0AC44  (DHSD_ECOLI) -  Succinate dehydrogenase hydrophobic membrane anchor subunit from Escherichia coli (strain K12)

Seq: 115 a.a.

Struc: 105 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.1.3.5.1 - succinate dehydrogenase.
• Pathway: Citric acid cycle
• Reaction: a quinone + succinate = fumarate + a quinol

quinone (Bound ligand (Het Group name = TEO) matches with 88.89% similarity) + succinate = 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

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.