Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase

Acta Crystallographica. Section F, Structural Biology Communications
Lisa BuddrusSusan J Crennell

Abstract

Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg2+ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P3221, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and t...Continue Reading

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Citations

Jan 27, 2021·Journal of the American Chemical Society·Karen SchrieverPer-Olof Syrén

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Methods Mentioned

BETA
gel-filtration
thermal shift
X-ray

Software Mentioned

REFMAC
MolProbity
BASEML
PRANK
PhyML
MUSCLE
SigmaPlot
Gblocks
BALBES
CODEML

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