PDBsum entry 4jzv

Hydrolase/RNA

PDB id: 4jzv

Contents

Protein chains

158 a.a.

Ligands

GCP-_DG

EPE

Metals

_MG ×3

Waters ×70

PDB id:

4jzv

Name:

Hydrolase/RNA

Title:

Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp- pgpg) - second guanosine residue in guanosine binding pocket

Structure:

RNA pyrophosphohydrolase. Chain: a, b. Synonym: 8-oxo-dgtpase, 7,8-dihydro-8-oxoguanine-triphosphatase, dgtp pyrophosphohydrolase. Engineered: yes. RNA (5'-r( (Gcp)p G)-3'). Chain: c. Engineered: yes

Source:

Bacillus subtilis subsp. Subtilis. Organism_taxid: 224308. Strain: 168. Gene: bsu30630, mutta, ytkd. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes

Resolution:

2.20Å R-factor: 0.221 R-free: 0.241

Authors:

J.Piton,V.Larue,Y.Thillier,A.Dorleans,O.Pellegrini,I.Li De La Sierra- Gallay,J.J.Vasseur,F.Debart,C.Tisne,C.Condon

Key ref:

J.Piton et al. (2013). Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates. Proc Natl Acad Sci U S A, 110, 8858-8863. PubMed id: 23610407 DOI: 10.1073/pnas.1221510110

Date:

03-Apr-13 Release date: 08-May-13

Protein chains

O35013  (YTKD_BACSU) -  Putative 8-oxo-dGTP diphosphatase YtkD from Bacillus subtilis (strain 168)

Seq: 158 a.a.

Struc: 158 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.55 - 8-oxo-dGTP diphosphatase.
• Reaction: 8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate + H⁺

8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate (Bound ligand (Het Group name = GCP) matches with 53.33% similarity) + H(+)

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1073/pnas.1221510110

Proc Natl Acad Sci U S A 110:8858-8863 (2013)

PubMed id: 23610407

Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.

J.Piton, V.Larue, Y.Thillier, A.Dorléans, O.Pellegrini, I.Li de la Sierra-Gallay, J.J.Vasseur, F.Debart, C.Tisné, C.Condon.

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.