3P4P

Crystal structure of Menaquinol:fumarate oxidoreductase in complex with fumarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

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This is version 1.3 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:  
    3P4P, 3P4Q, 3P4R, 3P4S

  • 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 specificity presents a challenge in this system ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase flavoprotein subunitA,
E [auth M]
577Escherichia coli 042Mutation(s): 0 
Gene Names: frdAEC042_4630
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00363 (Escherichia coli (strain K12))
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Go to UniProtKB:  P00363
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase iron-sulfur proteinB,
F [auth N]
243Escherichia coli 536Mutation(s): 0 
Gene Names: ECP_4399
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0AC47 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AC47
Entity Groups  
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UniProt GroupP0AC47
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase subunit CC,
G [auth O]
130Escherichia coli DH1Mutation(s): 0 
Gene Names: frdCEcDH1_3838
Membrane Entity: Yes 
UniProt
Find proteins for P0A8Q0 (Escherichia coli (strain K12))
Explore P0A8Q0 
Go to UniProtKB:  P0A8Q0
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UniProt GroupP0A8Q0
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate reductase subunit DD,
H [auth P]
119Escherichia coli DH1Mutation(s): 0 
Gene Names: frdDEcDH1_3839
Membrane Entity: Yes 
UniProt
Find proteins for P0A8Q3 (Escherichia coli (strain K12))
Explore P0A8Q3 
Go to UniProtKB:  P0A8Q3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8Q3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
I [auth A],
N [auth M]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
M [auth B],
Q [auth N]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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L [auth B],
P [auth N]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
K [auth B],
O [auth N]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FUM
Query on FUM

Download Ideal Coordinates CCD File 
J [auth A]FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.317α = 90
b = 137.633β = 90
c = 270.684γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-15
    Changes: Non-polymer description
  • Version 1.3: 2017-11-08
    Changes: Refinement description