2PYU

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP

2PYU の概要

• エントリーDOI: 10.2210/pdb2pyu/pdb
• 関連するPDBエントリー: 1K7K 2Q16
• 分子名称: Inosine Triphosphate Pyrophosphatase RdgB, INOSINIC ACID, 1,2-ETHANEDIOL, ... (4 entities in total)
• 機能のキーワード: itp pyrophosphatase x-ray structure enzyme mechanism product, hydrolase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23745.57

構造登録者

Singer, A.U.,Proudfoot, M.,Skarina, T.,Savchenko, A.,Yakunin, A.F. (登録日: 2007-05-16, 公開日: 2008-03-18, 最終更新日: 2023-08-30)

主引用文献

Savchenko, A.,Proudfoot, M.,Skarina, T.,Singer, A.,Litvinova, O.,Sanishvili, R.,Brown, G.,Chirgadze, N.,Yakunin, A.F.
Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.
J.Mol.Biol., 374:1091-1103, 2007

PubMed Abstract: Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases.

PubMed: 17976651
DOI: 10.1016/j.jmb.2007.10.012

実験手法

X-RAY DIFFRACTION (2.02 Å)