cd09859

PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 residues in 53EXO PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA/RNA binding. The active site includes a set of conserved acidic residues that are essential for binding divalent metal ions required for nuclease activity.