4JZU

Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - first guanosine residue in guanosine binding pocket

Summary for 4JZU

• Entry DOI: 10.2210/pdb4jzu/pdb
• Related: 4JZS 4JZT 4JZV
• Descriptor: RNA PYROPHOSPHOHYDROLASE, RNA (5'-R(*(GCP)P*G)-3'), 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: nudix hydrolase, rna pyrophosphohydrolase, rpph, cytosol, hydrolase, hydrolase-rna complex, hydrolase/rna
• Biological source: Bacillus subtilis subsp. subtilis
• Total number of polymer chains: 3
• Total formula weight: 38122.23

Authors

Piton, J.,Larue, V.,Thillier, Y.,Dorleans, A.,Pellegrini, O.,Li de la Sierra-Gallay, I.,Vasseur, J.J.,Debart, F.,Tisne, C.,Condon, C. (deposition date: 2013-04-03, release date: 2013-05-08, Last modification date: 2024-04-03)

Primary citation

Piton, J.,Larue, V.,Thillier, Y.,Dorleans, A.,Pellegrini, O.,Li de la Sierra-Gallay, I.,Vasseur, J.J.,Debart, F.,Tisne, C.,Condon, C.
Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.
Proc.Natl.Acad.Sci.USA, 110:8858-8863, 2013

PubMed Abstract: The initiation of mRNA degradation often requires deprotection of its 5' end. In eukaryotes, the 5'-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5'-monophosphorylated RNA that is a substrate for 5' exoribonucleases. In bacteria, the 5'-triphosphate group of primary transcripts is also converted to a 5' monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5' exoribonucleases. Here we present the crystal structures of Bacillus subtilis RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to Bdellovibrio bacteriovorus RppH, which recognizes the first nucleotide of its RNA targets, the B. subtilis enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria.

PubMed: 23610407
DOI: 10.1073/pnas.1221510110

Experimental method

X-RAY DIFFRACTION (1.7 Å)