› 1vdx

X-ray diffraction
2.4Å resolution

Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase

Released:
DOI: 10.2210/pdb1vdx/pdb
PDB entry 1vdx coloured by chain, front view.
PDB entry 1vdx coloured by chain, side view.
PDB entry 1vdx coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii.
Rehse PH, Tahirov TH
Acta Crystallogr D Biol Crystallogr 61 1207-12 (2005)
PMID: 16131753

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: 21.13 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O57823 (Residues: 1-184; Coverage: 100%)
Gene name: PH0099
Sequence domains: LigT like Phosphoesterase
Structure domains: Cyclic phosphodiesterase

Ligands and Environments

1 bound ligand:
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 44.068Å b: 45.471Å c: 93.171Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.225 0.274
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology.
Chambers et al. (2015)
5 other articles

5 mentions without citation

AKAP18 contains a phosphoesterase domain that binds AMP.
Gold et al. (2008)
4 more