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 beta. Second, on the basis of sequence homology between topo V and polymerase beta, 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 (ii) 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.
Belova
G I
GI
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia.
Prasad
R
R
Kozyavkin
S A
SA
Lake
J A
JA
Wilson
S H
SH
Slesarev
A I
AI
D000595:Amino Acid Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D004260:DNA Repair; D004264:DNA Topoisomerases, Type I / Q000378:metabolism*; D019605:Euryarchaeota / Q000201:enzymology; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014443:Tyrosine / Q000378:metabolism
D014443:Tyrosine; C082698:DNA topoisomerase V; D004264:DNA Topoisomerases, Type I