› 4s2y

X-ray diffraction
1.6Å resolution

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

Released:
DOI: 10.2210/pdb4s2y/pdb
PDB entry 4s2y coloured by chain, front view.
PDB entry 4s2y coloured by chain, side view.
PDB entry 4s2y coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structures of RNA complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5'-end-dependent mRNA decay.
Vasilyev N, Serganov A
J Biol Chem 290 9487-99 (2015)
PMID: 25657011

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-141546 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
RNA pyrophosphohydrolase Chain: A
Molecule details ›
Chain: A
Length: 161 amino acids
Theoretical weight: 18.97 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A776 (Residues: 1-160; Coverage: 91%)
Gene names: JW2798, b2830, nudH, rppH, ygdP
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase
RNA (5'-R(*(APC)*GP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 3 nucleotides
Theoretical weight: 1.09 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand CL 1 x CL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 79.631Å b: 36.484Å c: 58.073Å
α: 90° β: 102.3° γ: 90°
R-values:
R R work R free
0.174 0.172 0.198
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

The complex enzymology of mRNA decapping: Enzymes of four classes cleave pyrophosphate bonds.
Kramer et al. (2019)
6 more

9 mentions without citation

Nudix hydrolases degrade protein-conjugated ADP-ribose.
Daniels et al. (2015)
8 more