Lakol et al.,

ABSTRACT
Bacillus licheniformis YdaP gene encodes for pyruvate oxidase (EC: 1.2.3.3), a key enzyme which catalyzes the oxidative decarboxylation of pyruvate into acetate and CO2 . The objective of this study is to predict the YdaP protein structure, by comparison with known X-ray structures and using bioinformatics tools. The three-dimensional model structure of the B. licheniformis YdaP enzyme was constructed using the sequence of L. plantarum POX as the template. The model structure of B. licheniformis YdaP showed positional conservation of amino acid residues Asp313 and Ala314, compared with other members of the pyruvate oxidase family. The model structure of B. licheniformis YdaP showed that residues Met466, Ile467 and Glu470 were located on an α-helix connecting to loops in the active cavity. These residues are presumably critical for the catalytic activity of pyruvate oxidases, and have been proposed to be involved in substrate binding. The overall topology of the B. licheniformis YdaP was similar to known pyruvate oxidase crystal structures. The structure of the ThDP motif was identical to that found in the other pyruvate oxidases. However, analysis of the substrate binding cavity showed one major difference. Bulky hydrophobic amino acid residues Tyr469, His476 and Tyr479 formed part of active site cavity. In L. plantarum POX, these correspond to amino acid residues Trp479, Ile480 and Glu483. This observation suggested that these residues would negatively influence the accessibility of large substrates (e.g., aromatic) into the catalytic center. This information may assist in studies aimed at engineering the catalytic active site of the enzyme to improve accessibility of larger substrates to the active site.

Keywords: Active site, Bacillus licheniformis, Homology modeling, Protein structure, Pyruvate oxidase, Three-dimensional structure,
YdaP enzyme

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