3P4S

Crystal structure of Menaquinol:fumarate oxidoreductase in complex with a 3-nitropropionate adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase.

Tomasiak, T.M.Archuleta, T.L.Andrell, J.Luna-Chavez, C.Davis, T.A.Sarwar, M.Ham, A.J.McDonald, W.H.Yankovskaya, V.Stern, H.A.Johnston, J.N.Maklashina, E.Cecchini, G.Iverson, T.M.

(2011) J.Biol.Chem. 286: 3047-3056

  • DOI: 10.1074/jbc.M110.192849
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Complex II superfamily members catalyze the kinetically difficult interconversion of succinate and fumarate. Due to the relative simplicity of complex II substrates and their similarity to other biologically abundant small molecules, substrate specif ...

    Complex II superfamily members catalyze the kinetically difficult interconversion of succinate and fumarate. Due to the relative simplicity of complex II substrates and their similarity to other biologically abundant small molecules, substrate specificity presents a challenge in this system. In order to identify determinants for on-pathway catalysis, off-pathway catalysis, and enzyme inhibition, crystal structures of Escherichia coli menaquinol:fumarate reductase (QFR), a complex II superfamily member, were determined bound to the substrate, fumarate, and the inhibitors oxaloacetate, glutarate, and 3-nitropropionate. Optical difference spectroscopy and computational modeling support a model where QFR twists the dicarboxylate, activating it for catalysis. Orientation of the C2-C3 double bond of activated fumarate parallel to the C(4a)-N5 bond of FAD allows orbital overlap between the substrate and the cofactor, priming the substrate for nucleophilic attack. Off-pathway catalysis, such as the conversion of malate to oxaloacetate or the activation of the toxin 3-nitropropionate may occur when inhibitors bind with a similarly activated bond in the same position. Conversely, inhibitors that do not orient an activatable bond in this manner, such as glutarate and citrate, are excluded from catalysis and act as inhibitors of substrate binding. These results support a model where electronic interactions via geometric constraint and orbital steering underlie catalysis by QFR.


    Organizational Affiliation

    Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase flavoprotein subunit
A, M
577Escherichia coli (strain K12)Mutation(s): 0 
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 5 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

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Download CCD File 
B, N
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
3NP
Query on 3NP

Download SDF File 
Download CCD File 
A
3-NITROPROPANOIC ACID
C3 H5 N O4
WBLZUCOIBUDNBV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.065α = 90.00
b = 139.006β = 90.00
c = 276.476γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance