Premium
Crystal structure of pyruvate decarboxylase from Zymobacter palmae
Author(s) -
Buddrus Lisa,
Andrews Emma S. V.,
Leak David J.,
Danson Michael J.,
Arcus Vickery L.,
Crennell Susan J.
Publication year - 2016
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.572
H-Index - 37
ISSN - 2053-230X
DOI - 10.1107/s2053230x16012012
Subject(s) - pyruvate decarboxylase , chemistry , decarboxylation , dimer , thiamine pyrophosphate , tetramer , stereochemistry , cofactor , biochemistry , alcohol dehydrogenase , enzyme , organic chemistry , catalysis
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate‐ and Mg 2+ ion‐dependent enzyme that catalyses the non‐oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Å resolution. They belonged to space group P 2 1 , with unit‐cell parameters a = 204.56, b = 177.39, c = 244.55 Å and R r.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were R work = 0.186 (0.271 in the highest resolution bin) and R free = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions.