A type IB topoisomerase with DNA repair activities

doi:10.1073/pnas.111040498

A type IB topoisomerase with DNA repair activities

^*Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia; ^†Laboratory of Structural Biology, National Institute on Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; ^¶Fidelity Systems, Inc., Gaithersburg, MD 20879; and ^§Molecular Biology Institute, University of California, Los Angeles, CA 90095

Edited by James C. Wang, Harvard University, Cambridge, MA, and approved March 16, 2001 (received for review January 24, 2001)

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 β. Second, on the basis of sequence homology between topo V and polymerase β, 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.

Footnotes

↵ ‖ To whom reprint requests should be addressed at: Fidelity Systems, Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879. E-mail: alex{at}fidelitysystems.com.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The sequence reported in this paper has been deposited in the GenBank database (accession no. AF311944).
Abbreviations:

HhH,

helix-hairpin-helix;

HTH,

helix-turn-helix;

dRP,

2-deoxyribose 5-phosphate;

AP,

apurinic/apyrimidinic;

topo V,

topoisomerase V;

β-pol,

polymerase β