› 8dcb

X-ray diffraction
2.6Å resolution

RNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ and GTP

Released:
DOI: 10.2210/pdb8dcb/pdb
PDB entry 8dcb coloured by chain, front view.
PDB entry 8dcb coloured by chain, side view.
PDB entry 8dcb coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
Jacewicz A, Dantuluri S, Shuman S
OpenAccess logo RNA (2022)
PMID: 36130078

Function and Biology Details

Reaction catalysed: 
(1a) GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-N(tau)-phosphono-L-histidine + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129837 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Pho hyp2 intein Chains: A, B
Molecule details ›
Chains: A, B
Length: 501 amino acids
Theoretical weight: 55.75 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O59245 (Residues: 406-486, 487-871; Coverage: 53%)
Gene names: PH1602, rtcB
Sequence domains: tRNA-splicing ligase RtcB

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
5 bound ligands:
Ligand GTP 2 x GTP
Ligand GOL 1 x GOL
Ligand NI 5 x NI
Ligand SO4 10 x SO4
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 81.241Å b: 137.492Å c: 149.559Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.209
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Insights into the structure and function of the RNA ligase RtcB.
Moncan et al. (2023)