› 1vgj

X-ray diffraction
1.94Å resolution

Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii

Released:
DOI: 10.2210/pdb1vgj/pdb
PDB entry 1vgj coloured by chain, front view.
PDB entry 1vgj coloured by chain, side view.
PDB entry 1vgj coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
The structure of Pyrococcus horikoshii 2'-5' RNA ligase at 1.94 A resolution reveals a possible open form with a wider active-site cleft.
Gao YG, Yao M, Okada A, Tanaka I
Acta Crystallogr Sect F Struct Biol Cryst Commun 62 1196-200 (2006)
PMID: 17142895

Function and Biology Details

Reaction catalysed: 
(Ribonucleotide)(n)-2',3'-cyclic phosphate + H(2)O = (ribonucleotide)(n)-2'-phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129618 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA 2',3'-cyclic phosphodiesterase Chain: A
Molecule details ›
Chain: A
Length: 184 amino acids
Theoretical weight: 21.27 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O57823 (Residues: 1-184; Coverage: 100%)
Gene name: PH0099
Sequence domains: LigT like Phosphoesterase
Structure domains: Cyclic phosphodiesterase

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 3 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: P212121
Unit cell:
a: 41.5Å b: 45.7Å c: 97.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.21 0.265
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Structural and functional evolution of 2',3'-cyclic nucleotide 3'-phosphodiesterase.
Myllykoski et al. (2016)
1 more

5 mentions without citation

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification.
Mroczek et al. (2012)
4 more