A Model for the Mechanism of Human Topoisomerase I

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Science  06 Mar 1998:
Vol. 279, Issue 5356, pp. 1534-1541
DOI: 10.1126/science.279.5356.1534

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The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22–base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of the enzyme that contact DNA. The linker region that connects the central core of the enzyme to the carboxyl-terminal domain assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme. The positively charged DNA-proximal surface of the linker makes only a few contacts with the DNA downstream of the cleavage site. In combination with the crystal structures of the reconstituted human topoisomerase I before and after DNA cleavage, this information suggests which amino acid residues are involved in catalyzing phosphodiester bond breakage and religation. The structures also lead to the proposal that the topoisomerization step occurs by a mechanism termed “controlled rotation.”

  • * These authors contributed equally to this work.

  • Present address: Emerald BioStructures, Incorporated, 7865 Northeast Day Road West, Bainbridge Island, WA 98110, USA. E-mail: emerald_biostructures{at}

  • Present address: Department of Structural Biology, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.

  • § To whom correspondence should be addressed: E-mail: champoux{at}

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