5C8L

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase

5C8L の概要

• エントリーDOI: 10.2210/pdb5c8l/pdb
• 関連するPDBエントリー: 5C7Q 5C7T
• 分子名称: NudF protein, alpha-D-glucopyranose, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: nudix, hydrolase
• 由来する生物種: Bdellovibrio bacteriovorus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 43992.12

構造登録者

Gabelli, S.B.,de la Pena, A.H.,Suarez, A.,Amzel, L.M. (登録日: 2015-06-25, 公開日: 2016-01-20, 最終更新日: 2023-09-27)

主引用文献

de la Pena, A.H.,Suarez, A.,Duong-Ly, K.C.,Schoeffield, A.J.,Pizarro-Dupuy, M.A.,Zarr, M.,Pineiro, S.A.,Amzel, L.M.,Gabelli, S.B.
Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.
Plos One, 10:e0141716-e0141716, 2015

PubMed Abstract: Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.

PubMed: 26524597
DOI: 10.1371/journal.pone.0141716

実験手法

X-RAY DIFFRACTION (1.8 Å)