6VCR

Crystal structure of E.coli RppH in complex with CTP

6VCR の概要

• エントリーDOI: 10.2210/pdb6vcr/pdb
• 関連するPDBエントリー: 6VCK 6VCL 6VCM 6VCN 6VCO 6VCP 6VCQ
• 分子名称: RNA pyrophosphohydrolase, CYTIDINE-5'-TRIPHOSPHATE, PYROPHOSPHATE, ... (5 entities in total)
• 機能のキーワード: rna degradation, rna binding protein
• 由来する生物種: Escherichia coli S88
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 20689.28

構造登録者

Gao, A.,Vasilyev, N.,Kaushik, A.,Duan, W.,Serganov, A. (登録日: 2019-12-21, 公開日: 2020-02-05, 最終更新日: 2023-10-11)

主引用文献

Gao, A.,Vasilyev, N.,Kaushik, A.,Duan, W.,Serganov, A.
Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Nucleic Acids Res., 48:3776-3788, 2020

PubMed Abstract: All enzymes face a challenge of discriminating cognate substrates from similar cellular compounds. Finding a correct substrate is especially difficult for the Escherichia coli Nudix hydrolase RppH, which triggers 5'-end-dependent RNA degradation by removing orthophosphate from the 5'-diphosphorylated transcripts. Here we show that RppH binds and slowly hydrolyzes NTPs, NDPs and (p)ppGpp, which each resemble the 5'-end of RNA. A series of X-ray crystal structures of RppH-nucleotide complexes, trapped in conformations either compatible or incompatible with hydrolysis, explain the low reaction rates of mononucleotides and suggest two distinct mechanisms for their hydrolysis. While RppH adopts the same catalytic arrangement with 5'-diphosphorylated nucleotides as with RNA, the enzyme hydrolyzes 5'-triphosphorylated nucleotides by extending the active site with an additional Mg2+ cation, which coordinates another reactive nucleophile. Although the average intracellular pH minimizes the hydrolysis of nucleotides by slowing their reaction with RppH, they nevertheless compete with RNA for binding and differentially inhibit the reactivity of RppH with triphosphorylated and diphosphorylated RNAs. Thus, E. coli RppH integrates various signals, such as competing non-cognate substrates and a stimulatory protein factor DapF, to achieve the differential degradation of transcripts involved in cellular processes important for the adaptation of bacteria to different growth conditions.

PubMed: 31960065
DOI: 10.1093/nar/gkaa024

実験手法

X-RAY DIFFRACTION (1.6 Å)