Mechanochemical analysis of DNA gyrase using rotor bead tracking

Nature

Volumn 439, Issue 7072, 2006, Pages 100-104

  Gore, Jeff ^a   Bryant, Zev ^a,b,d   Stone, Michael D ^a,e   Nöllmann, Marcelo ^a   Cozzarelli, Nicholas R ^a   Bustamante, Carlos ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d STANFORD UNIVERSITY   (United States)

^e HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINETRIPHOSPHATE; ENZYME KINETICS; ENZYMES; HYDROLYSIS; ROTATION;

CHIRAL WRAPPING; DNA GYRASE; NEGATIVE SUPERCOILS; PICONEWTONS; ROTOR BEAD TRACKING;

DNA;

ADENOSINE TRIPHOSPHATE; DNA; DNA TOPOISOMERASE (ATP HYDROLYSING);

BIOLOGY;

ANALYTIC METHOD; ARTICLE; CHEMICAL MODEL; DISSOCIATION; DNA SUPERCOILING; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ASSAY; ENZYME KINETICS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; ROTATION; TENSION; VELOCITY;

EID: 30144434477     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature04319     Document Type: Article

References (29)

1. Gellert, M., Mizuuchi, K., O'Dea, M. H. & Nash, H. A. DNA gyrase: an enzyme that introduces superhelical turns into DNA. Proc. Natl Acad. Sci. USA 73, 3872-3876 (1976).
2. Champoux, J. J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369-413 (2001).
3. Corbett, K. D. & Berger, J. M. Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct. 33, 95-118 (2004).
4. Liu, L. F. & Wang, J. C. DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell 15, 979-984 (1978).
5. Liu, L. F. & Wang, J. C. Micrococcus luteus DNA gyrase: active components and a model for its supercoiling of DNA. Proc. Natl Acad. Sci. USA 75, 2098-2102 (1978).
6. Reece, R. J. & Maxwell, A. The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Nucleic Acids Res. 19, 1399-1405 (1991).
7. Corbett, K. D., Shultzaberger, R. K. & Berger, J. M. The C-terminal domain of DNA gyrase A adopts a DNA-bending β-pinwheel fold. Proc. Natl Acad. Sci. USA 101, 7293-7298 (2004).
8. Ruthenburg, A. J., Graybosch, D. M., Huetsch, J. C. & Verdine, G. L. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J. Biol. Chem. 280, 26177-26184 (2005).
9. Kampranis, S. C. & Maxwell, A. Conversion of DNA gyrase into a conventional type II topoisomerase. Proc. Natl Acad. Sci. USA 93, 14416-14421 (1996).
10. Bryant, Z. et al. Structural transitions and elasticity from torque measurements on DNA. Nature 424, 338-341 (2003).
11. Brown, P. O. & Cozzarelli, N. R. A sign inversion mechanism for enzymatic supercoiling of DNA. Science 206, 1081-1083 (1979).
12. Levine, C., Hiasa, H. & Marians, K. J. DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochim. Biophys. Acta 1400, 29-43 (1998).
13. Wang, J. C. Cellular roles of DNA topoisomerases: a molecular perspective. Nature Rev. Mol. Cell. Biol. 3, 430-440 (2002).
14. Charvin, G., Strick, T. R., Bensimon, D. & Croquette, V. Tracking topoisomerase activity at the single-molecule level. Annu. Rev. Biophys. Biomol. Struct. 34, 201-219 (2005).
15. Bates, A. D. & Maxwell, A. DNA Topology (Oxford Univ. Press, Oxford, 2005).
16. Heddle, J. G., Mitelheiser, S., Maxwell, A. & Thomson, N. H. Nucleotide binding to DNA gyrase causes loss of DNA wrap. J. Mol. Biol. 337, 597-610 (2004).
17. Kampranis, S. C., Bates, A. D. & Maxwell, A. A model for the mechanism of strand passage by DNA gyrase. Proc. Natl Acad Sci. USA 96, 8414-8419 (1999).
18. Smith, S. B., Finzi, L. & Bustamante, C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 1122-1126 (1992).
19. Strick, T. R., Allemand, J. F., Bensimon, D., Bensimon, A. & Croquette, V. The elasticity of a single supercoiled DNA molecule. Science 271, 1835-1837 (1996).
20. Wang, M. D. et al. Force and velocity measured for single molecules of RNA polymerase. Science 282, 902-907 (1998).
21. Keller, D. & Bustamante, C. The mechanochemistry of molecular motors. Biophys. J. 78, 541-556 (2000).
22. 1-ATPase. Nature 410, 898-904 (2001).
23. Uemura, S., Higuchi, H., Olivares, A. O., De La Cruz, E. M. & Ishiwata, S. Mechanochemical coupling of two substeps in a single myosin V motor. Nature Struct. Mol. Biol. 11, 877-883 (2004).
24. Roca, J. & Wang, J. C. The capture of a DNA double helix by an ATP-dependent protein clamp: a key step in DNA transport by type II DNA topoisomerases. Cell 71, 833-840 (1992).
25. Baird, C. L., Harkins, T. T., Morris, S. K. & Lindsley, J. E. Topoisomerase II drives DNA transport by hydrolyzing one ATP. Proc. Natl Acad. Sci. USA 96, 13685-13690 (1999).
26. Pease, P. J. et al. Sequence-directed DNA translocation by purified FtsK. Science 307, 586-590 (2005).
27. Block, S. M. Leading the procession: new insights into kinesin motors. J. Cell Biol. 140, 1281-1284 (1998).
28. Vale, R. D. Myosin V motor proteins: marching stepwise towards a mechanism. J. Cell Biol. 163, 445-450 (2003).
29. Pato, M. L., Howe, M. M. & Higgins, N. P. A DNA gyrase-binding site at the center of the bacteriophage μ genome is required for efficient replicative transposition. Proc. Natl Acad. Sci. USA 87, 8716-8720 (1990).