2WVG

Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas mobilis

Summary for 2WVG

• Entry DOI: 10.2210/pdb2wvg/pdb
• Related: 1ZPD 2WVH
• Descriptor: PYRUVATE DECARBOXYLASE, FLUORIDE ION, 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYL TRIHYDROGEN DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: thiamine diphosphate, lyase, flavoprotein, metal-binding, alcohol fermentation
• Biological source: ZYMOMONAS MOBILIS
• Total number of polymer chains: 4
• Total formula weight: 245767.50

Authors

Pei, X.Y.,Erixon, K.,Luisi, B.F.,Leeper, F.J. (deposition date: 2009-10-16, release date: 2010-02-09, Last modification date: 2023-12-20)

Primary citation

Pei, X.Y.,Erixon, K.,Luisi, B.F.,Leeper, F.J.
Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase from Zymomonas Mobilis
Biochemistry, 49:1727-, 2010

PubMed Abstract: 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.

PubMed: 20099870
DOI: 10.1021/BI901864J

Experimental method

X-RAY DIFFRACTION (1.75 Å)