5CB5

Structural Insights into the Mechanism of Escherichia coli Ymdb

5CB5 の概要

• エントリーDOI: 10.2210/pdb5cb5/pdb
• 関連するPDBエントリー: 5CB3
• 分子名称: O-acetyl-ADP-ribose deacetylase, ADENOSINE-5-DIPHOSPHORIBOSE, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: deacetylase, adpr, oaadpr, macro domain, hydrolase
• 由来する生物種: Escherichia coli K12
• タンパク質・核酸の鎖数: 18
• 化学式量合計: 365599.19

構造登録者

Zhang, W.,Wang, C.,Song, Y.,Shao, C.,Zhang, X.,Zang, J. (登録日: 2015-06-30, 公開日: 2015-11-04, 最終更新日: 2023-11-08)

主引用文献

Zhang, W.,Wang, C.,Song, Y.,Shao, C.,Zhang, X.,Zang, J.
Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase
J.Struct.Biol., 192:478-486, 2015

PubMed Abstract: The Escherichia coli protein YmdB belongs to the macrodomain protein family, which can bind ADP-ribose (ADPr) and its derivatives. Recently, YmdB was reported to be capable of deacetylating O-acetyl-ADP-ribose (OAADPr) to yield ADPr and free acetate. To study the substrate specificity and catalytic mechanism, the crystal structures of E. coli YmdB in complex with ADPr, double mutant N25AD35A complexed with 2'-OAADPr, and Y126A/ADPr complex were solved at 1.8Å, 2.8Å and 3.0Å resolution, respectively. Structural and biochemical studies reveal that YmdB has substrate specificity against 2'-OAADPr. The conserved residues Asn25 and Asp35 are crucial for catalytic activity, and an active water molecule is proposed as the nucleophile to attack the acetyl group of 2'-OAADPr. Our findings indicate that the conserved phenyl group of Tyr126 plays a crucial role in catalytic activity by stabilizing the right orientation of distal ribose and that Gly32 may be important for activity by interacting with the acetyl group of 2'-OAADPr. Based on these observations, a model of YmdB in complex with 2'-OAADPr was made to illustrate the proposed catalytic mechanism of YmdB.

PubMed: 26481419
DOI: 10.1016/j.jsb.2015.10.010

実験手法

X-RAY DIFFRACTION (2.8 Å)