4S2V

E. coli RppH structure, KI soak

Summary for 4S2V

• Entry DOI: 10.2210/pdb4s2v/pdb
• Related: 4S2W 4S2X 4S2Y
• Descriptor: RNA pyrophosphohydrolase, IODIDE ION, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: nudix hydrolase, rna pyrophosphohydrolase, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 22148.91

Authors

Vasilyev, N.,Serganov, A. (deposition date: 2015-01-23, release date: 2015-02-11, Last modification date: 2024-02-28)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.7 Å)