3P4S: Crystal Structure Of Menaquinol:fumarate Oxidoreductase In Complex With A 3-Nitropropionate Adduct

Citation:
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. 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.
PDB ID: 3P4SDownload
MMDB ID: 87212
PDB Deposition Date: 2010/10/7
Updated in MMDB: 2010/12
Experimental Method:
x-ray diffraction
Resolution: 3.1  Å
Source Organism:
Escherichia coli O55:H7 str. CB9615
Similar Structures:
Biological Unit for 3P4S: tetrameric; determined by author and by software (PISA)
Molecular Components in 3P4S
Label Count Molecule
Proteins (4 molecules)
1
Fumarate Reductase Flavoprotein Subunit
Molecule annotation
1
Fumarate Reductase Iron-sulfur Subunit
Molecule annotation
1
Fumarate Reductase Subunit C
Molecule annotation
1
Fumarate Reductase Subunit D
Molecule annotation
Chemicals (5 molecules)
1
1
2
1
3
1
4
1
5
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.