5IW5

Crystal structure of E. coli NudC in complex with NMN

5IW5 の概要

• エントリーDOI: 10.2210/pdb5iw5/pdb
• 関連するPDBエントリー: 5IW4
• 分子名称: NADH pyrophosphatase, ZINC ION, BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: nmn, rna, capping, nudix, hydrolase
• 由来する生物種: Escherichia coli B354
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 60425.31

構造登録者

Li, S.,Du, J.,Patel, D.J. (登録日: 2016-03-22, 公開日: 2016-07-13, 最終更新日: 2023-11-08)

主引用文献

Hofer, K.,Li, S.,Abele, F.,Frindert, J.,Schlotthauer, J.,Grawenhoff, J.,Du, J.,Patel, D.J.,Jaschke, A.
Structure and function of the bacterial decapping enzyme NudC
Nat.Chem.Biol., 12:730-734, 2016

PubMed Abstract: RNA capping and decapping are thought to be distinctive features of eukaryotes. The redox cofactor NAD was recently discovered to be attached to small regulatory RNAs in bacteria in a cap-like manner, and Nudix hydrolase NudC was found to act as a NAD-decapping enzyme in vitro and in vivo. Here, crystal structures of Escherichia coli NudC in complex with substrate NAD and with cleavage product NMN reveal the catalytic residues lining the binding pocket and principles underlying molecular recognition of substrate and product. Biochemical mutation analysis identifies the conserved Nudix motif as the catalytic center of the enzyme, which needs to be homodimeric, as the catalytic pocket is composed of amino acids from both monomers. NudC is single-strand specific and has a purine preference for the 5'-terminal nucleotide. The enzyme strongly prefers NAD-linked RNA (NAD-RNA) over NAD and binds to a diverse set of cellular RNAs in an unspecific manner.

PubMed: 27428510
DOI: 10.1038/nchembio.2132

実験手法

X-RAY DIFFRACTION (2.7 Å)