› 4jzv

X-ray diffraction
2.2Å resolution

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

Released:
DOI: 10.2210/pdb4jzv/pdb
PDB entry 4jzv coloured by chain, front view.
PDB entry 4jzv coloured by chain, side view.
PDB entry 4jzv coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.
Piton J, Larue V, Thillier Y, Dorléans A, Pellegrini O, Li de la Sierra-Gallay I, Vasseur JJ, Debart F, Tisné C, Condon C
Proc Natl Acad Sci U S A 110 8858-63 (2013)
PMID: 23610407

Function and Biology Details

Reaction catalysed: 
8-oxo-dGTP + H(2)O = 8-oxo-dGMP + diphosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-128643 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Putative 8-oxo-dGTP diphosphatase YtkD Chains: A, B
Molecule details ›
Chains: A, B
Length: 158 amino acids
Theoretical weight: 18.54 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O35013 (Residues: 1-158; Coverage: 100%)
Gene names: BSU30630, mutTA, ytkD
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase
RNA (5'-R(*(GCP)P*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 2 nucleotides
Theoretical weight: 803 Da
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21212
Unit cell:
a: 62.158Å b: 138.025Å c: 35.684Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.22 0.241
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 review citations

Initiation of mRNA decay in bacteria.
Laalami et al. (2014)
7 more

3 mentions without citation

Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.
Piton et al. (2013)
2 more