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Nucleic Acids Res. 2015 Dec 15;43(22):11031-46. doi: 10.1093/nar/gkv1073. Epub 2015 Oct 20.

Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I.

Author information

1
Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA ktan@anl.gov.
2
Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.
3
Department of Biochemistry and Molecular Biology, Basic Science Building, New York Medical College, Valhalla, NY 10595, USA.
4
Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA.
5
Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA ytsedinh@fiu.edu.

Abstract

Escherichia coli topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. A full length structure of E. coli topoisomerase I reported here shows how the C-terminal domains bind single-stranded DNA (ssDNA) to recognize the accumulation of negative supercoils in duplex DNA. These C-terminal domains of E. coli topoisomerase I are known to interact with RNA polymerase, and two flexible linkers within the C-terminal domains may assist in the movement of the ssDNA for the rapid removal of transcription driven negative supercoils. The structure has also unveiled for the first time how the 4-Cys zinc ribbon domain and zinc ribbon-like domain bind ssDNA with primarily π-stacking interactions. This novel structure, in combination with new biochemical data, provides important insights into the mechanism of genome regulation by type IA topoisomerases that is essential for life, as well as the structures of homologous type IA TOP3α and TOP3β from higher eukaryotes that also have multiple 4-Cys zinc ribbon domains required for their physiological functions.

PMID:
26490962
PMCID:
PMC4678816
DOI:
10.1093/nar/gkv1073
[Indexed for MEDLINE]
Free PMC Article

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