Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA

Kay Perry; Alfonso Mondragón

doi:10.1016/j.str.2003.09.013

Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA

Kay Perry, Alfonso Mondragón^*

^*Corresponding author for this work

Molecular Biosciences

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

38 Scopus citations

Abstract

In order to gain insights into the mechanism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.

Original language	English (US)
Pages (from-to)	1349-1358
Number of pages	10
Journal	Structure
Volume	11
Issue number	11
DOIs	https://doi.org/10.1016/j.str.2003.09.013
State	Published - Nov 2003

Funding

We thank A. Changela and B. Taneja for their comments and suggestions. Research was supported by NIH Grant GM51350. Support from the R.H. Lurie Cancer Center of Northwestern University to the Structural Biology Facility is acknowledged. Portions of this work were performed at the DuPont-Northwestern-Dow collaborative Access Team (DND-CAT) Synchrotron Research Center at the Advanced Photon Source (APS) and at the Stanford Synchrotron Radiation Laboratory (SSRL). DND-CAT is supported by DuPont, Dow, and the NSF, and use of the APS is supported by the DOE. SSRL is operated by the DOE, Office of Basic Energy Sciences. The SSRL Biotechnology Program is supported by the NIH and the DOE.

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1016/j.str.2003.09.013

Cite this

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title = "Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA",

abstract = "In order to gain insights into the mechanism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.",

author = "Kay Perry and Alfonso Mondrag{\'o}n",

note = "Funding Information: We thank A. Changela and B. Taneja for their comments and suggestions. Research was supported by NIH Grant GM51350. Support from the R.H. Lurie Cancer Center of Northwestern University to the Structural Biology Facility is acknowledged. Portions of this work were performed at the DuPont-Northwestern-Dow collaborative Access Team (DND-CAT) Synchrotron Research Center at the Advanced Photon Source (APS) and at the Stanford Synchrotron Radiation Laboratory (SSRL). DND-CAT is supported by DuPont, Dow, and the NSF, and use of the APS is supported by the DOE. SSRL is operated by the DOE, Office of Basic Energy Sciences. The SSRL Biotechnology Program is supported by the NIH and the DOE. ",

year = "2003",

month = nov,

doi = "10.1016/j.str.2003.09.013",

language = "English (US)",

volume = "11",

pages = "1349--1358",

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AU - Perry, Kay

AU - Mondragón, Alfonso

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N2 - In order to gain insights into the mechanism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.

AB - In order to gain insights into the mechanism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.

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Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA

Abstract

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Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I

Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3'

Cite this

Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA

Abstract

Funding

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Datasets

Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I

Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3'

Cite this