9HS2

Crystal structure of the Escherichia coli nucleosidase PpnN (ppGpp form)

これはPDB形式変換不可エントリーです。

9HS2 の概要

• エントリーDOI: 10.2210/pdb9hs2/pdb
• 分子名称: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, GUANOSINE-5',3'-TETRAPHOSPHATE, 9-deazaguanosine-5'-monophosphate (3 entities in total)
• 機能のキーワード: ppgpp, nucleosidase, gmp, hydrolase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 209642.59

構造登録者

Baerentsen, R.L.,Brodersen, D.E. (登録日: 2024-12-18, 公開日: 2025-11-12, 最終更新日: 2026-01-21)

主引用文献

Baerentsen, R.L.,Kronborg, K.,Brodersen, D.E.,Zhang, Y.E.
Catalytic mechanism and differential alarmone regulation of a conserved stringent nucleosidase.
Structure, 34:198-209.e4, 2026

PubMed Abstract: Insights into bacterial metabolic adaptation during stress is crucial for understanding early mechanisms of antibiotic resistance. In the Gram-negative bacterium Escherichia coli, the universal stringent response produces the alarmones (p)ppGpp that target many cellular proteins. The cellular nucleosidase PpnN is regulated by (p)ppGpp and was shown to balance bacterial fitness and persistence during fluoroquinolone exposure. pppGpp and ppGpp both activate PpnN, but differentially regulate its cooperativity via an unknown mechanism; furthermore, the catalytic mechanism of PpnN has remained unclear. Here, we provide mechanistic insights into the interaction of PpnN with a substrate analogue, reaction products, and alarmone molecules, which allows us to understand the catalytic mechanism of this family of nucleosidases and the differential modes of regulation by ppGpp and pppGpp, respectively. Comparison to the homologous plant cytokinin-producing LOG proteins reveals that PpnN utilizes an evolutionarily conserved purine hydrolysis mechanism, which in bacteria is regulated by alarmones during stress.

PubMed: 41197623
DOI: 10.1016/j.str.2025.10.012

実験手法

X-RAY DIFFRACTION (3.4 Å)