PDBsum entry 1e7p

Oxidoreductase

PDB id: 1e7p

Contents

Protein chains

655 a.a. *

239 a.a. *

254 a.a. *

Ligands

FAD ×4

MLA ×4

FES ×4

F3S ×4

SF4 ×4

HEM ×8

LMT ×4

Metals

_NA ×4

* Residue conservation analysis

PDB id:

1e7p

Name:

Oxidoreductase

Title:

Quinol:fumarate reductase from wolinella succinogenes

Structure:

Fumarate reductase flavoprotein subunit. Chain: a, d, g, j. Engineered: yes. Other_details: 8-alpha-[-n-epsilon-histidyl] covalent bond between flavin adenine dinucleotide (fad) and his 43. Fumarate reductase iron-sulfur subunit. Chain: b, e, h, k. Engineered: yes. Fumarate reductase cytochrome b subunit.

Source:

Wolinella succinogenes. Vibrio succinogenes. Organism_taxid: 844. Gene: frda, ws0831. Expressed in: wolinella succinogenes. Expression_system_taxid: 844. Gene: frdb, ws0830. Strain: atcc 29543 / dsm 1740 / lmg 7466 / nctc 11488 / fdc 602w. Variant: frdc-e66q.

Biol. unit:

Hexamer (from PQS)

Resolution:

3.10Å R-factor: 0.283 R-free: 0.291

Authors:

C.R.D.Lancaster,A.Kroeger

Key ref:

C.R.Lancaster et al. (2001). A third crystal form of Wolinella succinogenes quinol:fumarate reductase reveals domain closure at the site of fumarate reduction. Eur J Biochem, 268, 1820-1827. PubMed id: 11248702 DOI: 10.1046/j.1432-1327.2001.02053.x

Date:

01-Sep-00 Release date: 09-Apr-01

Protein chains

P17412  (FRDA_WOLSU) -  Fumarate reductase flavoprotein subunit from Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)

Seq: 656 a.a.

Struc: 655 a.a.

Protein chains

P17596  (FRDB_WOLSU) -  Fumarate reductase iron-sulfur subunit from Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)

Seq: 239 a.a.

Struc: 239 a.a.

Protein chains

P17413  (FRDC_WOLSU) -  Fumarate reductase cytochrome b subunit from Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)

Seq: 256 a.a.

Struc: 254 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

quinone + succinate (Bound ligand (Het Group name = MLA) matches with 50.00% similarity) = 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: 10.1046/j.1432-1327.2001.02053.x

Eur J Biochem 268:1820-1827 (2001)

PubMed id: 11248702

A third crystal form of Wolinella succinogenes quinol:fumarate reductase reveals domain closure at the site of fumarate reduction.

C.R.Lancaster, R.Gross, J.Simon.

ABSTRACT

Quinol:fumarate reductase (QFR) is a membrane protein complex that couples the reduction of fumarate to succinate to the oxidation of quinol to quinone. Previously, the crystal structure of QFR from Wolinella succinogenes was determined based on two different crystal forms, and the site of fumarate binding in the flavoprotein subunit A of the enzyme was located between the FAD-binding domain and the capping domain [Lancaster, C.R.D., Kröger, A., Auer, M., & Michel, H. (1999) Nature 402, 377--385]. Here we describe the structure of W. succinogenes QFR based on a third crystal form and refined at 3.1 A resolution. Compared with the previous crystal forms, the capping domain is rotated in this structure by approximately 14 degrees relative to the FAD-binding domain. As a consequence, the topology of the dicarboxylate binding site is much more similar to those of membrane-bound and soluble fumarate reductase enzymes from other organisms than to that found in the previous crystal forms of W. succinogenes QFR. This and the effects of the replacement of Arg A301 by Glu or Lys by site-directed mutagenesis strongly support a common mechanism for fumarate reduction in this superfamily of enzymes.

Selected figure(s)

Figure 2.
Fig. 2. The site of fumarate reduction in subunit A (stereo views). The QFR crystal form ‘C’ Arg A301 carbon atoms are drawn in pink and its nitrogen atoms in light blue. (A) Electron density maps from the refined model of crystal form ‘C’ at 3.1 Å resolution. Contour levels are 1.0 (2F[o] - F[c,] blue) and 3.0 (F[o] - F[c,] green, with the malonate molecule omitted from the phase calculation). Due to insufficient density in the 2F[o] - F[c] map, the side chain of Arg A301 has been assigned zero occupancy. See text for details. (B) Comparison of W. succinogenes QFR crystal forms ‘C’ (PDB entry 1E7P, carbon atoms in yellow, complex with malonate) and ‘B’ (PDB entry 1QLB, carbon atoms in green, complex with fumarate). The isolated red spheres correspond to the oxygen atoms of two water molecules in PDB entry 1QLB. (C) Comparison of the crystal structures of the fumarate reducing sites in W. succinogenes QFR crystal form ‘C’ (PDB entry 1E7P, carbon atoms in yellow), in E. coli QFR (PDB entry 1FUM, carbon atoms in white), and in the S. frigidimarina soluble flavocytochrome c[3] (PDB entry 1QJD, carbon atoms in grey). The different dicarboxylate compounds included in the models are malonate (1E7P), oxaloacetate (1FUM), and a malate-like intermediate (1QJD). Residues are numbered according to W. succinogenes QFR.

Figure 3.
Fig. 3. Possible mechanism of fumarate reduction in W. succinogenes QFR involving the residues shown in Fig. 2 Go-. Hydride transfer from the N5 of FAD to the -methenyl of fumarate (in blue) is coupled to proton transfer to the position of the substrate from the side chain of Arg A301.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2001, 268, 1820-1827) copyright 2001.

Figures were selected by an automated process.