Structural and biochemical analyses of the metallo-β-lactamase fold protein Yhfl from Bacillus subtilis

초록

Metallo-beta-lactamase (MBL) fold proteins play critical roles in diverse biological processes, such as DNA repair, RNA processing, detoxification, and metabolism. Although MBL fold proteins share a metal-bound alpha beta beta alpha structure, they are highly heterogeneous in metal type, metal coordination, and oligomerization and exhibit different catalytic functions. Bacillus subtilis contains the yhfl gene, which is predicted to encode an MBL fold protein. To reveal the structural and functional features of Yhfl, we determined two crystal structures of Yhfl and biochemically characterized the catalytic activity of Yhfl. Yhfl forms an alpha-chelix-decorated beta-sandwich structure and assembles into a dimer using highly conserved residues. Each Yhfl chain simultaneously interacts with two metal ions, which are coordinated by histidine and aspartate residues that are strictly conserved in Yhfl orthologs. A comparative analysis of Yhfl and its homologous structures suggests that Yhfl would function as a phosphodiesterase. Indeed, Yhfl drove the phosphodiesterase reaction and showed high catalytic activity at pH 8.0-9.5 in the presence of manganese. Moreover, we propose that the active site of Yhfl is located at a metal-containing pocket generated between the two subunits of a Yhfl dimer. (C) 2019 Elsevier Inc. All rights reserved.

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