2B76

E. coli Quinol fumarate reductase FrdA E49Q mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fumarate Reductase and Succinate Oxidase Activity of Escherichia coli Complex II Homologs Are Perturbed Differently by Mutation of the Flavin Binding Domain

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

(2006) J.Biol.Chem. 281: 11357-11365

  • DOI: 10.1074/jbc.M512544200

  • PubMed 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 ca ...

    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.


    Organizational Affiliation

    Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase flavoprotein subunit
A, M
602Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: frdA
EC: 1.3.5.4
Find proteins for P00363 (Escherichia coli (strain K12))
Go to UniProtKB:  P00363
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase iron-sulfur protein
B, N
243Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: frdB
EC: 1.3.5.1
Find proteins for P0AC47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase subunit C
C, O
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: frdC
Find proteins for P0A8Q0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8Q0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase subunit D
D, P
119Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: frdD
Find proteins for P0A8Q3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8Q3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B, N
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
B, N
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, M
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
B, N
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MQ7
Query on MQ7

Download SDF File 
Download CCD File 
D, P
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A, M
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.802α = 90.00
b = 139.527β = 90.00
c = 273.972γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance