4S2X

Structure of E. coli RppH bound to RNA and two magnesium ions

4S2X の概要

• エントリーDOI: 10.2210/pdb4s2x/pdb
• 関連するPDBエントリー: 4S2V 4S2W 4S2Y
• 分子名称: RNA pyrophosphohydrolase, RNA (5'-R(*(APC)*GP*U)-3'), MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: nudix hydrolase, rna pyrophosphohydrolase, hydrolase-rna complex, hydrolase/rna
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 20300.12

構造登録者

Vasilyev, N.,Serganov, A. (登録日: 2015-01-23, 公開日: 2015-02-11, 最終更新日: 2023-09-20)

主引用文献

Vasilyev, N.,Serganov, A.
Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay.
J.Biol.Chem., 290:9487-9499, 2015

PubMed Abstract: 5'-End-dependent RNA degradation impacts virulence, stress responses, and DNA repair in bacteria by controlling the decay of hundreds of mRNAs. The RNA pyrophosphohydrolase RppH, a member of the Nudix hydrolase superfamily, triggers this degradation pathway by removing pyrophosphate from the triphosphorylated RNA 5' terminus. Here, we report the x-ray structures of Escherichia coli RppH (EcRppH) in apo- and RNA-bound forms. These structures show distinct conformations of EcRppH·RNA complexes on the catalytic pathway and suggest a common catalytic mechanism for Nudix hydrolases. EcRppH interacts with RNA by a bipartite mechanism involving specific recognition of the 5'-terminal triphosphate and the second nucleotide, thus enabling discrimination against mononucleotides as substrates. The structures also reveal the molecular basis for the preference of the enzyme for RNA substrates bearing guanine in the second position by identifying a protein cleft in which guanine interacts with EcRppH side chains via cation-π contacts and hydrogen bonds. These interactions explain the modest specificity of EcRppH at the 5' terminus and distinguish the enzyme from the highly selective RppH present in Bacillus subtilis. The divergent means by which RNA is recognized by these two functionally and structurally analogous enzymes have important implications for mRNA decay and the regulation of protein biosynthesis in bacteria.

PubMed: 25657011
DOI: 10.1074/jbc.M114.634824

実験手法

X-RAY DIFFRACTION (1.5 Å)