Crystal structure of pyruvate decarboxylase from Zymobacter palmae.
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 P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Å and Rr.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 Rwork = 0.186 (0.271 in the highest resolution bin) and Rfree = 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.
Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England.
Lisa
L
Buddrus
School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
Emma S V
ES
Andrews
Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England.
David J
DJ
Leak
Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England.
Michael J
MJ
Danson
School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
Vickery L
VL
Arcus
Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England.
Susan J
SJ
Crennell
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D002413:Cations, Divalent; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D019855:Ethylene Glycol / Q000737:chemistry; D015870:Gene Expression; D044129:Halomonadaceae / Q000737:chemistry* / Q000201:enzymology; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D011767:Pyruvate Decarboxylase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019289:Pyruvic Acid / Q000737:chemistry* / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D013835:Thiamine Pyrophosphate / Q000737:chemistry* / Q000378:metabolism
D001426:Bacterial Proteins; D002413:Cations, Divalent; D011994:Recombinant Proteins; D019289:Pyruvic Acid; D011767:Pyruvate Decarboxylase; D019855:Ethylene Glycol; D008274:Magnesium; D013835:Thiamine Pyrophosphate
TPP-dependent enzyme; Zymobacter palmae; crystal structure; lyase; pyruvate decarboxylase