PDBsum entry 2bs3

Oxidoreductase

PDB id: 2bs3

Contents

Protein chains

656 a.a. *

239 a.a. *

255 a.a. *

Ligands

FAD ×2

CIT ×2

FES ×2

F3S ×2

SF4 ×2

HEM ×4

LMT ×2

Metals

_NA ×2

Waters ×991

* Residue conservation analysis

PDB id:

2bs3

Name:

Oxidoreductase

Title:

Glu c180 -> gln variant quinol:fumarate reductase from wolinella succinogenes

Structure:

Quinol-fumarate reductase flavoprotein subunit a. Chain: a, d. Other_details: fad covalently bound to his a43 by an 8-alpha-(n- epsilon-histidyl) bond. Quinol-fumarate reductase iron-sulfur subunit b. Chain: b, e. Quinol-fumarate reductase diheme cytochrome b subunit c. Chain: c, f. Ec: 1.3.99.1

Source:

Wolinella succinogenes. Organism_taxid: 844. Organism_taxid: 844

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.19Å R-factor: 0.183 R-free: 0.198

Authors:

C.R.D.Lancaster

Key ref:

C.R.Lancaster et al. (2005). Experimental support for the "E pathway hypothesis" of coupled transmembrane e- and H+ transfer in dihemic quinol:fumarate reductase. Proc Natl Acad Sci U S A, 102, 18860-18865. PubMed id: 16380425 DOI: 10.1073/pnas.0509711102

Date:

14-May-05 Release date: 13-Dec-05

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: 656 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: 255 a.a.*

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

Enzyme reactions

• Enzyme class 2: Chains A, B, D, E: 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 = CIT) matches with 61.54% similarity) = fumarate + quinol

• Cofactor: FAD; Iron-sulfur

FAD (Bound ligand (Het Group name = FAD) corresponds exactly) Iron-sulfur

• Enzyme class 3: Chains C, F: E.C.1.3.99.1 - Deleted entry.
• Reaction: Succinate + acceptor = fumarate + reduced acceptor
• Cofactor: FAD

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0509711102

Proc Natl Acad Sci U S A 102:18860-18865 (2005)

PubMed id: 16380425

Experimental support for the "E pathway hypothesis" of coupled transmembrane e- and H+ transfer in dihemic quinol:fumarate reductase.

C.R.Lancaster, U.S.Sauer, R.Gross, A.H.Haas, J.Graf, H.Schwalbe, W.Mäntele, J.Simon, M.G.Madej.

ABSTRACT

Reconciliation of apparently contradictory experimental results obtained on the quinol:fumarate reductase, a diheme-containing respiratory membrane protein complex from Wolinella succinogenes, was previously obtained by the proposal of the so-called "E pathway hypothesis." According to this hypothesis, transmembrane electron transfer via the heme groups is strictly coupled to cotransfer of protons via a transiently established pathway thought to contain the side chain of residue Glu-C180 as the most prominent component. Here we demonstrate that, after replacement of Glu-C180 with Gln or Ile by site-directed mutagenesis, the resulting mutants are unable to grow on fumarate, and the membrane-bound variant enzymes lack quinol oxidation activity. Upon solubilization, however, the purified enzymes display approximately 1/10 of the specific quinol oxidation activity of the wild-type enzyme and unchanged quinol Michaelis constants, K(m). The refined x-ray crystal structures at 2.19 A and 2.76 A resolution, respectively, rule out major structural changes to account for these experimental observations. Changes in the oxidation-reduction heme midpoint potential allow the conclusion that deprotonation of Glu-C180 in the wild-type enzyme facilitates the reoxidation of the reduced high-potential heme. Comparison of solvent isotope effects indicates that a rate-limiting proton transfer step in the wild-type enzyme is lost in the Glu-C180 --> Gln variant. The results provide experimental evidence for the validity of the E pathway hypothesis and for a crucial functional role of Glu-C180.

Selected figure(s)

Figure 1.
Fig. 1. Electron and proton transfer in fumarate respiration (a) and W. succinogenes QFR (b and c). Positive and negative sides of the membrane are the periplasm and the cytoplasm, respectively. Figs. 1, 2, and 3 were prepared with a version of MOLSCRIPT (39) modified for color ramping (40) and map drawing (41) capabilities. (a) The key enzymes involved in fumarate respiration are indicated. (b) Hypothetical transmembrane electrochemical potential generation as suggested by the essential role of Glu-C66 for menaquinol oxidation by W. succinogenes QFR (16). The prosthetic groups of the W. succinogenes QFR dimer are displayed (coordinate set 1QLA, ref. 14). Distances between prosthetic groups are edge-to-edge distances in Å as defined by Page et al. (42). Also indicated are the side chain of Glu-C66 and a model of menaquinol (MKH[2]) binding. The position of bound fumarate (Fum) is taken from PDB ID code 1QLB [PDB] (14). (c) Hypothetical cotransfer of one H+ per electron across the membrane (E pathway hypothesis). The two protons that are liberated upon oxidation of menaquinol (MKH[2]) are released to the periplasm (bottom) via the residue Glu-C66. In compensation, coupled to electron transfer via the two heme groups, protons are transferred from the periplasm via the ring C propionate of the distal heme b[D] and the residue Glu-C180 to the cytoplasm (top), where they replace those protons that are bound during fumarate reduction. In the oxidized state of the enzyme, the E pathway is blocked.

Figure 4.
Fig. 4. The coupling of electron and proton flow in anaerobic (a and b) and aerobic SQRs respiration (c and d), respectively. Positive and negative sides of the membrane are described for Fig. 1. (a and b) Electroneutral reactions as catalyzed by diheme-containing QFR from W. succinogenes (a) and the hemeless QFR from E. coli. (b) MK and MKH[2], menaquinone and menaquinol, respectively. (c) Utilization of a transmembrane electrochemical potential as possibly catalyzed by diheme-containing SQR enzymes. (d) Electroneutral reaction as catalyzed by monoheme-containing SQR enzymes (complex II). Q and QH[2], ubiquinone and ubiquinol, respectively.

Figures were selected by an automated process.