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NMR structure of the N-terminal domain of the replication initiator protein DnaA

  • Original Paper
  • Published:
Journal of Structural and Functional Genomics

Abstract

DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1–100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 ± 0.2 Å based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein–protein interactions essential for the initiation of DNA replication.

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Acknowledgements

We thank D. King for mass spectral analysis, and J. Erzberger, M. Mott, and J. Berger for helpful discussions. We also thank M. Doucleff for recording several spectra. T.J.L. acknowledges the University of California Biotechnology Research and Education Program for financial support. This work was supported by grant GM62412 to the Berkeley Structural Genomics Center from the National Institute of General Medical Sciences, National Institutes of Health. We also thank NSF (BBS87W134 and 0119304) and NIH (RR15756 and GM068933) for funding NMR equipment.

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Authors and Affiliations

  1. Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA

    Thomas J. Lowery, Jeffrey G. Pelton, John-Marc Chandonia, Rosalind Kim, Hisao Yokota & David E. Wemmer

  2. Department of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA

    Thomas J. Lowery & David E. Wemmer

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  1. Thomas J. Lowery
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  2. Jeffrey G. Pelton
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  3. John-Marc Chandonia
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Correspondence to David E. Wemmer.

Additional information

Thomas J. Lowery and Jeffrey G. Pelton contributed equally to this work.

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Lowery, T.J., Pelton, J.G., Chandonia, JM. et al. NMR structure of the N-terminal domain of the replication initiator protein DnaA. J Struct Funct Genomics 8, 11–17 (2007). https://doi.org/10.1007/s10969-007-9022-7

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  • DOI: https://doi.org/10.1007/s10969-007-9022-7

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