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We identify and characterize an end-healing enzyme,  Cth Pnkp, from  Clostridium thermocellum  that catalyzes the phosphorylation of 5′-OH termini of DNA or RNA polynucleotides and the dephosphorylation of 2′,3′ cyclic phosphate, 2′-phosphate, and 3′-phosphate ribonucleotides.  Cth Pnkp also catalyzes an autoadenylylation reaction via a polynucleotide ligase-type mechanism. These characteristics are consistent with a role in end-healing during RNA or DNA repair.  Cth Pnkp is a homodimer of an 870-amino-acid polypeptide composed of three catalytic domains: an N-terminal module that resembles the polynucleotide kinase domain of bacteriophage T4 Pnkp, a central metal-dependent phosphoesterase module, and a C-terminal module that resembles the nucleotidyl transferase domain of polynucleotide ligases. The distinctive feature of  Cth Pnkp vis-à-vis known RNA repair enzymes is that its 3′ end modification component belongs to the calcineurin-type phosphatase superfamily. It contains putative counterparts of the amino acids that form the dinuclear metal-binding site and the phosphate-binding site of bacteriophage λ phosphatase. As with λ phosphatase, the 2′,3′ cAMP phosphatase activity of  Cth Pnkp is specifically dependent on nickel or manganese. We identify homologs of  Cth Pnkp in other bacterial proteomes.

An end-healing enzyme from Clostridium thermocellum with 5′ kinase, 2′,3′ phosphatase, and adenylyltransferase activities