5VPN

E. coli Quinol fumarate reductase FrdA E245Q mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.22 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase.

Starbird, C.A.Maklashina, E.Sharma, P.Qualls-Histed, S.Cecchini, G.Iverson, T.M.

(2017) J Biol Chem 292: 12921-12933

  • DOI: 10.1074/jbc.M117.795120
  • Primary Citation of Related Structures:  
    5VPN

  • PubMed Abstract: 
  • The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flaviny ...

    The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a Δ sdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdA E245 residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdA E245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdA E245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdA E245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.


    Organizational Affiliation

    Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase flavoprotein subunitA, E585Escherichia coli K-12Mutation(s): 1 
Gene Names: frdAb4154JW4115
EC: 1.3.5.4
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Fumarate Reductase Complex FrdA, E245Q mutant
Find proteins for P00363 (Escherichia coli (strain K12))
Explore P00363 
Go to UniProtKB:  P00363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase iron-sulfur subunitB, F243Escherichia coli O157:H7Mutation(s): 0 
Gene Names: frdBZ5760ECs5134
EC: 1.3.5.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Fumarate Reductase Complex FrdA, E245Q mutant
Find proteins for P0AC49 (Escherichia coli O157:H7)
Explore P0AC49 
Go to UniProtKB:  P0AC49
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase subunit CC, G130Escherichia coli K-12Mutation(s): 0 
Gene Names: frdCb4152JW4113
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Fumarate Reductase Complex FrdA, E245Q mutant
Find proteins for P0A8Q0 (Escherichia coli (strain K12))
Explore P0A8Q0 
Go to UniProtKB:  P0A8Q0
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase subunit DD, H119Escherichia coli K-12Mutation(s): 0 
Gene Names: frdDb4151JW4112
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Fumarate Reductase Complex FrdA, E245Q mutant
Find proteins for P0A8Q3 (Escherichia coli (strain K12))
Explore P0A8Q3 
Go to UniProtKB:  P0A8Q3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, E
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
SF4
Query on SF4

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B, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
B, F
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

Download CCD File 
B, F
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.22 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.565α = 90
b = 138.134β = 90
c = 220.079γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Veterans AffairsUnited StatesBX001077
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM061606
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008320
National Science Foundation (NSF, United States)United StatesDGE:0909667
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM105404
High-End Instrumentation GrantUnited StatesS10OD018483

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence