Crystal structure of pyruvate decarboxylase from Zymobacter palmae

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• 作者：Lisa Buddrus ; Emma S. V. Andrews ; David J. Leak ; Michael J. Danson ; Vickery L. Arcus and Susan J. Crennell
• 关键词：Zymobacter palmae ; pyruvate decarboxylase ; lyase ; crystal structure ; TPP-dependent enzyme
• 刊名：Acta Crystallographica Section F
• 出版年：2016
• 出版时间：September 2016
• 年：2016
• 卷：72
• 期：9
• 页码：700-706
• 全文大小：622K
• ISSN：1744-3091

文摘

Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg²⁺ 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 P2₁, 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 f="http://scripts.iucr.org/cgi-bin/explore.cgi?pdbid=2vbi" rel="references:http://scripts.iucr.org/cgi-bin/explore.cgi?pdbid=2vbi">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.