1d6m Citations

The structure of Escherichia coli DNA topoisomerase III.

Structure 7 1373-83 (1999)
Cited: 38 times
EuropePMC logo PMID: 10574789

Abstract

Background

DNA topoisomerases are enzymes that change the topology of DNA. Type IA topoisomerases transiently cleave one DNA strand in order to pass another strand or strands through the break. In this manner, they can relax negatively supercoiled DNA and catenate and decatenate DNA molecules. Structural information on Escherichia coli DNA topoisomerase III is important for understanding the mechanism of this type of enzyme and for studying the mechanistic differences among different members of the same subfamily.

Results

The structure of the intact and fully active E. coli DNA topoisomerase III has been solved to 3.0 A resolution. The structure shows the characteristic fold of the type IA topoisomerases that is formed by four domains, creating a toroidal protein. There is remarkable structural similarity to the 67 kDa N-terminal fragment of E. coli DNA topoisomerase I, although the relative arrangement of the four domains is significantly different. A major difference is the presence of a 17 amino acid insertion in topoisomerase III that protrudes from the side of the central hole and could be involved in the catenation and decatenation reactions. The active site is formed by highly conserved amino acids, but the structural information and existing biochemical and mutagenesis data are still insufficient to assign specific roles to most of them. The presence of a groove in one side of the protein is suggestive of a single-stranded DNA (ssDNA)-binding region.

Conclusion

The structure of E. coli DNA topoisomerase III resembles the structure of E. coli DNA topoisomerase I except for the presence of a positively charged loop that may be involved in catenation and decatenation. A groove on the side of the protein leads to the active site and is likely to be involved in DNA binding. The structure helps to establish the overall mechanism for the type IA subfamily of topoisomerases with greater confidence and expands the structural basis for understanding these proteins.

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Reviews citing this publication (11)

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  14. Adenosine 5'-O-(3-thio)triphosphate (ATPgammaS) promotes positive supercoiling of DNA by T. maritima reverse gyrase. Jungblut SP, Klostermeier D. J. Mol. Biol. 371 197-209 (2007)
  15. Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways. Terekhova K, Gunn KH, Marko JF, Mondragón A. Nucleic Acids Res. 40 10432-10440 (2012)
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  17. Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I. Tan K, Zhou Q, Cheng B, Zhang Z, Joachimiak A, Tse-Dinh YC. Nucleic Acids Res. 43 11031-11046 (2015)
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  20. Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold. Tan K, Cao N, Cheng B, Joachimiak A, Tse-Dinh YC. J. Mol. Biol. 428 182-193 (2016)
  21. Bacillus cereus DNA topoisomerase I and IIIalpha: purification, characterization and complementation of Escherichia coli TopoIII activity. Li Z, Hiasa H, DiGate R. Nucleic Acids Res. 33 5415-5425 (2005)
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  25. Kinetic insights into the temperature dependence of DNA strand cleavage and religation by topoisomerase III from the hyperthermophile Sulfolobus solfataricus. Zhang J, Pan B, Li Z, Sheng Zhao X, Huang L. Sci Rep 7 5494 (2017)