3ty9

X-ray diffraction
3.12Å resolution

Crystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate

Released:
Primary publication:
The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.
Proc Natl Acad Sci U S A 109 2296-301 (2012)
PMID: 22308407

Function and Biology Details

Reaction catalysed:
(1a) ATP + [RNA ligase]-L-lysine = [RNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107082 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallophosphoesterase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 393 amino acids
Theoretical weight: 45.1 KDa
Source organism: Acetivibrio thermocellus ATCC 27405
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A3DJ38 (Residues: 479-870; Coverage: 45%)
Gene name: Cthe_2768
Sequence domains: PNKP adenylyltransferase domain, ligase domain
Structure domains: DNA ligase/mRNA capping enzyme

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 95.5Å b: 132.76Å c: 162.77Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.219 0.266
Expression system: Escherichia coli BL21(DE3)