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Insights into negative modulation of E. coli replication initiation from the structure of SeqA–hemimethylated DNA complex

Nature Structural Biology volume 9, pages 839–843 (2002)Cite this article

Abstract

The SeqA protein binds clusters of fully methylated or hemimethylated GATC sequences at oriC and negatively modulates the initiation of DNA replication. We find that SeqA can be proteolytically cleaved into an N-terminal multimerization and a C-terminal DNA-binding domain and have determined the crystal structure of the C-terminal domain in complex with a hemimethylated GATC site. SeqA makes direct hydrogen bonds and van der Waals contacts with the hemimethylated A-T base pair in addition to interactions with the surrounding bases and DNA backbone. The tetrameric protein–DNA complex found in the crystal suggests that SeqA binds multiple GATC sites on separate DNA duplexes, altering the overall DNA topology and sequestering oriC from replication initiation.

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Figure 1: Characterization of SeqA-N and SeqA-C.
Figure 2: Structure of the SeqA-C–DNA complex.
Figure 3: Recognition of hemimethylated GATC by SeqA-C.
Figure 4: Model of SeqA crosslinking DNA duplexes at oriC.

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Acknowledgements

We thank J. Campbell and K. Mizuuchi for intellectual contributions, Z. Dauter for synchrotron beamline support, T. Brendler and S. Austin for the pSS1 plasmid, and R. Craigie and D. Leahy for critical reading of the manuscript. A.G. is supported by the Human Frontiers Science Program Organization.

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  1. Qinghai Zhao

    Present address: Human Genome Sciences, Inc., Rockville, Maryland, 20850, USA

Authors and Affiliations

  1. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Alba Guarné, Qinghai Zhao, Rodolfo Ghirlando & Wei Yang

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  1. Alba Guarné
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Correspondence to Wei Yang.

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Guarné, A., Zhao, Q., Ghirlando, R. et al. Insights into negative modulation of E. coli replication initiation from the structure of SeqA–hemimethylated DNA complex. Nat Struct Mol Biol 9, 839–843 (2002). https://doi.org/10.1038/nsb857

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