6KNT

Crystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis (space group P4332)

6KNT の概要

• エントリーDOI: 10.2210/pdb6knt/pdb
• 関連するPDBエントリー: 6KNS
• 分子名称: Putative metal-dependent hydrolase, ZINC ION (3 entities in total)
• 機能のキーワード: enzyme, metallo-beta-lactamase fold protein, hydrolase
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 108848.69

構造登録者

Na, H.W.,Namgung, B.,Song, W.S.,Yoon, S.I. (登録日: 2019-08-07, 公開日: 2019-09-18, 最終更新日: 2023-11-22)

主引用文献

Na, H.W.,Namgung, B.,Song, W.S.,Yoon, S.I.
Structural and biochemical analyses of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis.
Biochem.Biophys.Res.Commun., 519:35-40, 2019

PubMed Abstract: Metallo-β-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 αββα structure, they are highly heterogeneous in metal type, metal coordination, and oligomerization and exhibit different catalytic functions. Bacillus subtilis contains the yhfI gene, which is predicted to encode an MBL fold protein. To reveal the structural and functional features of YhfI, we determined two crystal structures of YhfI and biochemically characterized the catalytic activity of YhfI. YhfI forms an α-helix-decorated β-sandwich structure and assembles into a dimer using highly conserved residues. Each YhfI chain simultaneously interacts with two metal ions, which are coordinated by histidine and aspartate residues that are strictly conserved in YhfI orthologs. A comparative analysis of YhfI and its homologous structures suggests that YhfI would function as a phosphodiesterase. Indeed, YhfI 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 YhfI is located at a metal-containing pocket generated between the two subunits of a YhfI dimer.

PubMed: 31481231
DOI: 10.1016/j.bbrc.2019.08.106

実験手法

X-RAY DIFFRACTION (2.5 Å)