2B76 | pdb_00002b76

E. coli Quinol fumarate reductase FrdA E49Q mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.284 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.238 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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 Biological Chem 281: 11357-11365

  • DOI: https://doi.org/10.1074/jbc.M512544200
  • Primary Citation Related Structures: 
    2B76

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 247.09 kDa 
  • Atom Count: 16,840 
  • Modeled Residue Count: 2,133 
  • Deposited Residue Count: 2,188 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate reductase flavoprotein subunitA,
E [auth M]
602Escherichia coliMutation(s): 1 
Gene Names: FrdA
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P00363 (Escherichia coli (strain K12))
Explore P00363 
Go to UniProtKB:  P00363
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00363
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate reductase iron-sulfur proteinB,
F [auth N]
243Escherichia coliMutation(s): 0 
Gene Names: frdB
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0AC47 (Escherichia coli (strain K12))
Explore P0AC47 
Go to UniProtKB:  P0AC47
Entity Groups
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UniProt GroupP0AC47
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate reductase subunit CC,
G [auth O]
130Escherichia coliMutation(s): 0 
Gene Names: frdC
Membrane Entity: Yes 
UniProt
Find proteins for P0A8Q0 (Escherichia coli (strain K12))
Explore P0A8Q0 
Go to UniProtKB:  P0A8Q0
Entity Groups
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UniProt GroupP0A8Q0
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate reductase subunit DD,
H [auth P]
119Escherichia coliMutation(s): 0 
Gene Names: frdD
Membrane Entity: Yes 
UniProt
Find proteins for P0A8Q3 (Escherichia coli (strain K12))
Explore P0A8Q3 
Go to UniProtKB:  P0A8Q3
Entity Groups
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UniProt GroupP0A8Q3
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
J [auth A],
P [auth M]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MQ7

Query on MQ7



Download:Ideal Coordinates CCD File
N [auth D],
T [auth P]
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
M [auth B],
S [auth N]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S



Download:Ideal Coordinates CCD File
L [auth B],
R [auth N]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FLC

Query on FLC



Download:Ideal Coordinates CCD File
I [auth A],
O [auth M]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
FES

Query on FES



Download:Ideal Coordinates CCD File
K [auth B],
Q [auth N]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.284 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.238 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.802α = 90
b = 139.527β = 90
c = 273.972γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description