3CIR

E. coli Quinol fumarate reductase FrdA T234A mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II.

Tomasiak, T.M.Maklashina, E.Cecchini, G.Iverson, T.M.

(2008) J.Biol.Chem. 283: 15460-15468

  • DOI: 10.1074/jbc.M801372200

  • PubMed Abstract: 
  • In Escherichia coli, the complex II superfamily members succinate:ubiquinone oxidoreductase (SQR) and quinol:fumarate reductase (QFR) participate in aerobic and anaerobic respiration, respectively. Complex II enzymes catalyze succinate and fumarate i ...

    In Escherichia coli, the complex II superfamily members succinate:ubiquinone oxidoreductase (SQR) and quinol:fumarate reductase (QFR) participate in aerobic and anaerobic respiration, respectively. Complex II enzymes catalyze succinate and fumarate interconversion at the interface of two domains of the soluble flavoprotein subunit, the FAD binding domain and the capping domain. An 11-amino acid loop in the capping domain (Thr-A234 to Thr-A244 in quinol:fumarate reductase) begins at the interdomain hinge and covers the active site. Amino acids of this loop interact with both the substrate and a proton shuttle, potentially coordinating substrate binding and the proton shuttle protonation state. To assess the loop's role in catalysis, two threonine residues were mutated to alanine: QFR Thr-A244 (act-T; Thr-A254 in SQR), which hydrogen-bonds to the substrate at the active site, and QFR Thr-A234 (hinge-T; Thr-A244 in SQR), which is located at the hinge and hydrogen-bonds the proton shuttle. Both mutations impair catalysis and decrease substrate binding. The crystal structure of the hinge-T mutation reveals a reorientation between the FAD-binding and capping domains that accompanies proton shuttle alteration. Taken together, hydrogen bonding from act-T to substrate may coordinate with interdomain motions to twist the double bond of fumarate and introduce the strain important for attaining the transition state.


    Organizational Affiliation

    Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, 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 subunit
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.861α = 90.00
b = 135.468β = 90.00
c = 266.024γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
ADSCdata collection
CNSphasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance