{
  "id": "pnk",
  "name": "Polynucleotide_kinase",
  "moa": "Adds a 5'-phosphate group to the 3'-OH end of the tRNA fragment cleaved by PrrC, making it ready for ligation.",
  "moa_category": "synthesises and restores essential molecules depleted by bacterial defence",
  "evidence": "Polynucleotide kinase (pnk) was shown to be essential for the repair of tRNAs cleaved by the T4-encoded anticodon nuclease. In T4-infected E. coli prr strains, specific tRNA fragments accumulated in infections with pnk mutants, while these fragments were transient during wild-type infection. This suggested that pnk activity was required to process and repair the cleavage products. Biochemical analysis of the cleavage termini revealed that pnk catalyzes conversion of 2':3'-cyclic phosphate and 5'-OH termini into 3'-OH and 5'-phosphate ends, creating substrates for RNA ligase. In vitro assays confirmed this, showing that only after incubation with purified pnk could the tRNA fragments be ligated by RNA ligase. Phosphatase digestion assays, thin-layer chromatography, and RNase T1 mapping of terminal groups provided direct evidence of enzymatic activity, specifically hydrolysis of 2':3'-cyclic phosphates and phosphorylation of 5'-OH ends, demonstrating the dual phosphatase and kinase roles of the pnk protein in tRNA repair.",
  "defence_subtype": "Escherichia coli PrrC",
  "doi": "10.1002/j.1460-2075.1987.tb02532.x",
  "multicomponent": "rna_ligase",
  "pdb": "1LY1",
  "structure_type": "PDB entry",
  "protein_source_name": "Enterobacteria phage T4",
  "protein_source_link": "https://www.ncbi.nlm.nih.gov/nuccore/NC_000866.4",
  "defences": [
    {
      "name": "PrrC",
      "link": "https://defensefinder.mdmlab.fr/wiki/defense-systems/prrc"
    }
  ],
  "pfam_annotations": [
    {
      "name": "AAA_33",
      "accession": "PF13671.12",
      "length": 143,
      "evalue": 5.4e-25,
      "hmm_from": 2,
      "hmm_to": 141,
      "ali_from": 5,
      "ali_to": 148,
      "env_from": 4,
      "env_to": 150
    },
    {
      "name": "HAD_PNKP",
      "accession": "PF25109.1",
      "length": 143,
      "evalue": 3e-61,
      "hmm_from": 1,
      "hmm_to": 143,
      "ali_from": 159,
      "ali_to": 301,
      "env_from": 159,
      "env_to": 301
    }
  ]
}