Structural Insights into the Prereaction State of Pyruvate Decarboxylase from Zymomonas mobilis,

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.

Auxin production by the plant trypanosomatidPhytomonas serpensand auxin homoeostasis in infected tomato fruits

“…The alignment also confirmed conservation of the localization of the four ionizable residues in PDC and IPDC proteins (Asp30; His116; His117; Glu481), which seem to play a more prominent role in catalysis than in substrate binding (Andrews and McLeish, 2012). The established 3D structures of pyruvatecomplexed Z. mobilis PDC (PDB ID 2wva; Pei et al 2010) and E. cloacae IPDC (PDB ID 1ovmA; Schütz et al 2003b) were used to infer the size of the active site of P. serpens enzyme and the location of potentially important residues (Fig. 6).…”

“…The overall quality of the models was assessed by Ramachandran plots using the RAMPAGE server (Lovell et al 2003). PyMOL (http://www.pymol.org) was used to visualize and align the established three-dimensional structures of E. cloacae IPDC (PDB ID 1ovmA, Schütz et al 2003b) and Z. mobilis PDC (PDB ID 2wva, Pei et al 2010).…”

Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations

“…By virtue of the neutral ring in place of the positively charged thiazolium ring, the authors suggested that this would serve as an electrostatic mimic of the carbene [57,58]. Later the thiazolium ring was replaced by a triazole ring in yet a different mimic of a neutral 5-membered ring [59].…”

Comparative proteome analysis of Aspergillus oryzae 3.042 and A. oryzae 100–8 strains: Towards the production of different soy sauce flavors

“…It is of interest to note that there was more AlcDH (spots 417, 418, 419 and 420), but less AldDH (spots 335, 336, 337 and 338)-this would suggest A100-8 produces more kinds of ethanols. Pyruvate decarboxylase (spots 158, 159, 160, 161 and 162) was more abundant in A100-8, and uses thiamine diphosphate as an essential cofactor to catalyze the formation of acetaldehyde in ethanol synthesis [42,43]. The over-production of ethanol is beneficial in the formation of flavor products such as esters.…”