Protein-nucleotide interactions in E. coli DNA topoisomerase I

Hadar Feinberg; Anita Changela; Alfonso Mondragón

doi:10.1038/13333

Protein-nucleotide interactions in E. coli DNA topoisomerase I

Hadar Feinberg, Anita Changela, Alfonso Mondragón^*

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

23 Scopus citations

Abstract

DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological states of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA, and hence it is likely that different regions of the enzyme bind DNA with different affinities. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa N-terminal fragment of Escherichia coli DNA topoisomerase I with mono- and trinucleotides. There are five different binding sites in the complexes, one of which is adjacent to the active site. Two other sites are in the central hole of the protein and may represent general DNA binding regions. The positions of these sites allow us to identify different DNA binding regions and to understand their possible roles in the catalytic cycle.

Original language	English (US)
Pages (from-to)	961-968
Number of pages	8
Journal	Nature Structural Biology
Volume	6
Issue number	10
DOIs	https://doi.org/10.1038/13333
State	Published - 1999

Funding

We acknowledge the contributions of C.D. Lima and A. Patera to the early stages of this project. We thank past and present members of the laboratory for help with data collection and for comments and suggestions. We also thank R. DiGate, L. Godley, M. Gwynn, T. Jardetzky, K. Perry, X. Qiu, A. Rosenzweig, A. Tackle, J. Widom, X. Yang and members of the Center of Structural Biology for comments and suggestions. We thank BNLS, CHESS, DND-CAT, and SSRL for access to their beamlines and help during data collection. We thank M. Blum of MAR USA for lending us the MAR CCD detector used at SSRL. This work was supported by the NIH (A.M.) and by SmithKline Beecham Pharmaceuticals. Portions of this work were performed at the DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) Synchrotron Research Center at the Advanced Photon Source, supported by DuPont, Dow, NSF and the State of Illinois. Use of the APS was supported by the DOE. Portions of this work were performed at SSRL, which is operated by the DOE. The SSRL Biotechnology Program is supported by the NIH and the DOE.

ASJC Scopus subject areas

Structural Biology
Biochemistry
Genetics

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10.1038/13333

Cite this

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abstract = "DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological states of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA, and hence it is likely that different regions of the enzyme bind DNA with different affinities. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa N-terminal fragment of Escherichia coli DNA topoisomerase I with mono- and trinucleotides. There are five different binding sites in the complexes, one of which is adjacent to the active site. Two other sites are in the central hole of the protein and may represent general DNA binding regions. The positions of these sites allow us to identify different DNA binding regions and to understand their possible roles in the catalytic cycle.",

author = "Hadar Feinberg and Anita Changela and Alfonso Mondrag{\'o}n",

note = "Funding Information: We acknowledge the contributions of C.D. Lima and A. Patera to the early stages of this project. We thank past and present members of the laboratory for help with data collection and for comments and suggestions. We also thank R. DiGate, L. Godley, M. Gwynn, T. Jardetzky, K. Perry, X. Qiu, A. Rosenzweig, A. Tackle, J. Widom, X. Yang and members of the Center of Structural Biology for comments and suggestions. We thank BNLS, CHESS, DND-CAT, and SSRL for access to their beamlines and help during data collection. We thank M. Blum of MAR USA for lending us the MAR CCD detector used at SSRL. This work was supported by the NIH (A.M.) and by SmithKline Beecham Pharmaceuticals. Portions of this work were performed at the DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) Synchrotron Research Center at the Advanced Photon Source, supported by DuPont, Dow, NSF and the State of Illinois. Use of the APS was supported by the DOE. Portions of this work were performed at SSRL, which is operated by the DOE. The SSRL Biotechnology Program is supported by the NIH and the DOE.",

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N2 - DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological states of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA, and hence it is likely that different regions of the enzyme bind DNA with different affinities. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa N-terminal fragment of Escherichia coli DNA topoisomerase I with mono- and trinucleotides. There are five different binding sites in the complexes, one of which is adjacent to the active site. Two other sites are in the central hole of the protein and may represent general DNA binding regions. The positions of these sites allow us to identify different DNA binding regions and to understand their possible roles in the catalytic cycle.

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Protein-nucleotide interactions in E. coli DNA topoisomerase I

Abstract

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ASJC Scopus subject areas

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COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'PTPTPT

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3'

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH TPTPTP3'

Cite this

Protein-nucleotide interactions in E. coli DNA topoisomerase I

Abstract

Funding

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Datasets

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'PTPTPT

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3'

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH TPTPTP3'

Cite this