A type IB topoisomerase with DNA repair activities

Previously we have characterized type IB DNA topoisomerase V (topo V) in the hyperthermophile Methanopyrus kandleri. The enzyme has a powerful topoisomerase activity and is abundant in M, kandleri. Here we report two characterizations of topo V, First, we found that its N-terminal domain has sequence homology with both eukaryotic type IB topoisomerases and the integrase family of tyrosine recombinases, The C-terminal part of the sequence includes 12 repeats, each repeat consisting of two similar but distinct helix-hairpin-helix motifs; the same arrangement is seen in recombination protein RuvA and mammalian DNA polymerase P, Second, on the basis of sequence homology between topo V and polymerase p, we predict and demonstrate that topo V possesses apurinic/ apyrimidinic (AP) site-processing activities that are important in base excision DNA repair: (i) it incises the phosphodiester backbone at the AP site, and Iib at the AP endonuclease cleaved AP site, it removes the 5 ' 2-deoxyribose 5-phosphate moiety so that a single-nucleotide gap with a 3 ' -hydroxyl and 5 ' -phosphate can be filled by a DNA polymerase. Topo V is thus the prototype for a new subfamily of type IB topoisomerases and is the first example of a topoisomerase with associated DNA repair activities.