› 4e6n

X-ray diffraction
2.39Å resolution

Crystal structure of bacterial Pnkp-C/Hen1-N heterodimer

Released:
DOI: 10.2210/pdb4e6n/pdb
PDB entry 4e6n coloured by chain, front view.
PDB entry 4e6n coloured by chain, side view.
PDB entry 4e6n coloured by chain, top view.
Source organism: Acetivibrio thermocellus ATCC 27405
Primary publication:
Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair.
Wang P, Chan CM, Christensen D, Zhang C, Selvadurai K, Huang RH
Proc Natl Acad Sci U S A 109 13248-53 (2012)
PMID: 22847431

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107079 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Metallophosphoesterase Chains: A, C
Molecule details ›
Chains: A, C
Length: 427 amino acids
Theoretical weight: 48.88 KDa
Source organism: Acetivibrio thermocellus ATCC 27405
Expression system: Escherichia coli
UniProt:
  • Canonical: A3DJ38 (Residues: 445-870; Coverage: 49%)
Gene name: Cthe_2768
Sequence domains: PNKP adenylyltransferase domain, ligase domain
Structure domains:
Small RNA 2'-O-methyltransferase Chains: B, D
Molecule details ›
Chains: B, D
Length: 230 amino acids
Theoretical weight: 26.24 KDa
Source organism: Acetivibrio thermocellus ATCC 27405
Expression system: Escherichia coli
UniProt:
  • Canonical: A3DJ37 (Residues: 1-230; Coverage: 50%)
Gene name: Cthe_2767
Sequence domains: RNA repair, ligase-Pnkp-associating, region of Hen1
Structure domains: Hen1, N-terminal domain

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand AMP 2 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P1
Unit cell:
a: 59.63Å b: 59.695Å c: 101.54Å
α: 81.38° β: 87.82° γ: 88.82°
R-values:
R R work R free
0.17 0.168 0.222
Expression system: Escherichia coli

Quick links

Citations

14 citation in other articles

Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.
Wang et al. (2012)
13 more

2 mentions without citation

Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair.
Wang et al. (2012)
1 more