2WVA: Structural Insights Into The Pre-Reaction State Of Pyruvate Decarboxylase From Zymomonas Mobilis

Pyruvate decarboxylase (PDC) uses thiamine diphosphate as an essential cofactor to catalyze the formation of acetaldehyde on the pathway of ethanol synthesis. Here we report the crystallographic image of a prereaction intermediate of a bacterial pyruvate decarboxylase prepared by cocrystallizing the enzyme with pyruvate and a stable analogue of the cofactor's activated ylid form. A second crystal structure of PDC in complex with fluoride shows that the ion organizes a water molecule that occludes the pyruvate binding site, accounting for the inhibitory effect of the halide. Also reported is a structure of the cofactor-free apo form, which when compared to the structure of the holo form indicates how thiamine diphosphate organizes the active site pocket of pyruvate decarboxylase to support catalysis. Guided by the structural and enzymatic data, we propose roles for several key residues in the catalytic mechanism.
PDB ID: 2WVADownload
MMDB ID: 79882
PDB Deposition Date: 2009/10/15
Updated in MMDB: 2011/10
Experimental Method:
x-ray diffraction
Resolution: 2.2  Å
Source Organism:
Similar Structures:
Biological Unit for 2WVA: tetrameric; determined by software (PISA)
Molecular Components in 2WVA
Label Count Molecule
Proteins (4 molecules)
Pyruvate Decarboxylase(Gene symbol: ZMOB_RS09070)
Molecule annotation
Chemicals (10 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB