A type IB topoisomerase with DNA repair activities

Proc Natl Acad Sci U S A. 2001 May 22;98(11):6015-20. doi: 10.1073/pnas.111040498. Epub 2001 May 15.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Cloning, Molecular
  • DNA Repair*
  • DNA Topoisomerases, Type I* / metabolism*
  • Euryarchaeota / enzymology
  • Humans
  • Molecular Sequence Data
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid
  • Tyrosine / metabolism

Substances

  • Tyrosine
  • DNA topoisomerase V
  • DNA Topoisomerases, Type I

Associated data

  • GENBANK/AF311944