PDBsum entry 2b76

Oxidoreductase

PDB id: 2b76

Contents

Protein chains

577 a.a. *

243 a.a. *

130 a.a. *

119 a.a. *

Ligands

FLC ×2

FAD ×2

FES ×2

F3S ×2

SF4 ×2

MQ7 ×2

* Residue conservation analysis

PDB id:

2b76

Name:

Oxidoreductase

Title:

E. Coli quinol fumarate reductase frda e49q mutation

Structure:

Fumarate reductase flavoprotein subunit. Chain: a, m. Engineered: yes. Mutation: yes. Fumarate reductase iron-sulfur protein. Chain: b, n. Engineered: yes. Fumarate reductase subunit c. Chain: c, o.

Source:

Escherichia coli. Organism_taxid: 562. Gene: frda. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: frdb. Gene: frdc. Gene: frdd.

Biol. unit:

Tetramer (from PQS)

Resolution:

3.30Å R-factor: 0.248 R-free: 0.284

Authors:

E.Maklashina,T.M.Iverson,Y.Sher,V.Kotlyar,O.Mirza,J.Andrell, J.M.Hudson,F.A.Armstrong,G.Cecchini

Key ref:

E.Maklashina et al. (2006). Fumarate reductase and succinate oxidase activity of Escherichia coli complex II homologs are perturbed differently by mutation of the flavin binding domain. J Biol Chem, 281, 11357-11365. PubMed id: 16484232 DOI: 10.1074/jbc.M512544200

Date:

03-Oct-05 Release date: 21-Feb-06

Protein chains

P00363  (FRDA_ECOLI) -  Fumarate reductase flavoprotein subunit from Escherichia coli (strain K12)

Seq: 602 a.a.

Struc: 577 a.a.*

Protein chains

P0AC47  (FRDB_ECOLI) -  Fumarate reductase iron-sulfur subunit from Escherichia coli (strain K12)

Seq: 244 a.a.

Struc: 243 a.a.

Protein chains

P0A8Q0  (FRDC_ECOLI) -  Fumarate reductase subunit C from Escherichia coli (strain K12)

Seq: 131 a.a.

Struc: 130 a.a.

Protein chains

P0A8Q3  (FRDD_ECOLI) -  Fumarate reductase subunit D from Escherichia coli (strain K12)

Seq: 119 a.a.

Struc: 119 a.a.

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

Enzyme reactions

• Enzyme class: Chains A, B, M, N: 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 = FLC) matches with 61.54% similarity) + succinate = fumarate + quinol

• Cofactor: FAD; Iron-sulfur

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

reference

DOI no: 10.1074/jbc.M512544200

J Biol Chem 281:11357-11365 (2006)

PubMed id: 16484232

Fumarate reductase and succinate oxidase activity of Escherichia coli complex II homologs are perturbed differently by mutation of the flavin binding domain.

E.Maklashina, T.M.Iverson, Y.Sher, V.Kotlyar, J.Andréll, O.Mirza, J.M.Hudson, F.A.Armstrong, R.A.Rothery, J.H.Weiner, G.Cecchini.

ABSTRACT

The Escherichia coli complex II homologues succinate:ubiquinone oxidoreductase (SQR, SdhCDAB) and menaquinol:fumarate oxidoreductase (QFR, FrdABCD) have remarkable structural homology at their dicarboxylate binding sites. Although both SQR and QFR can catalyze the interconversion of fumarate and succinate, QFR is a much better fumarate reductase, and SQR is a better succinate oxidase. An exception to the conservation of amino acids near the dicarboxylate binding sites of the two enzymes is that there is a Glu (FrdA Glu-49) near the covalently bound FAD cofactor in most QFRs, which is replaced with a Gln (SdhA Gln-50) in SQRs. The role of the amino acid side chain in enzymes with Glu/Gln/Ala substitutions at FrdA Glu-49 and SdhA Gln-50 has been investigated in this study. The data demonstrate that the mutant enzymes with Ala substitutions in either QFR or SQR remain functionally similar to their wild type counterparts. There were, however, dramatic changes in the catalytic properties when Glu and Gln were exchanged for each other in QFR and SQR. The data show that QFR and SQR enzymes are more efficient succinate oxidases when Gln is in the target position and a better fumarate reductase when Glu is present. Overall, structural and catalytic analyses of the FrdA E49Q and SdhA Q50E mutants suggest that coulombic effects and the electronic state of the FAD are critical in dictating the preferred directionality of the succinate/fumarate interconversions catalyzed by the complex II superfamily.

Selected figure(s)

Figure 2.
FIGURE 2. Menaquinol-fumarate reductase reaction catalyzed by QFR and FrdA E49Q. The reaction was assayed as described under "Materials and Methods" under anaerobic conditions in the presence of DT diaphorase and NADH to continuously regenerate MQ[1]H[2]. A, fumarate dependence of the rate of the MQ[1]H[2]-fumarate reductase reaction. B, reduction of 15 µM fumarate by wild type QFR and FrdA E49Q by MQ[1]H[2] regenerated in the presence of NADH and DT diaphorase. WT, wild type.

Figure 7.
FIGURE 7. Comparison of the active site structures in wild type (Protein Data Bank code 1KF6 [PDB] ) and FrdA E49Q QFR (Protein Data Bank code 2B76). The wild type (teal) and FrdA E49Q variant (yellow) are superimposed in the same view as Fig. 1. Only the main chains from the E49Q variant are shown for clarity. Oxygen atoms are in red, nitrogen atoms are in blue, and carbon atoms follow the color of the molecule. Little structural perturbation is observed, with a slight movement of the side chain functional group of Arg-287. However, an altered hydrogen-bonding pattern is observed, with a new hydrogen bonding interaction to the side chain of Glu-245, altered directionality of the hydrogen bond to Arg-287, and a putative hydrogen-bonding interaction with the N-5 of the FAD. The latter two have been shown to directly participate in the fumarate reduction reaction.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 11357-11365) copyright 2006.

Figures were selected by an automated process.