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Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB

Nature Structural Biology volume 7, pages 1139–1146 (2000)Cite this article

A Corrigendum to this article was published on 01 April 2005

Abstract

We have determined the high resolution NMR solution structure of the novel DNA binding domain of the Bacillus subtilis transition state regulator AbrB. Comparisons of the AbrB DNA binding domain with DNA binding proteins of known structure show that it is a member of a completely novel class of DNA recognition folds that employs a dimeric topology for cellular function. This new DNA binding conformation is referred to as the looped-hinge helix fold. Sequence homology investigations show that this DNA binding topology is found in other disparately related microbes. Structural analysis of the AbrB DNA binding domain together with bioanalytical and mutagenic data of full length AbrB allows us to construct a general model that describes the genetic regulation properties of AbrB.

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Figure 1: Stereo views of the high resolution solution structure of the AbrB N-terminal DNA binding domain.
Figure 2: Ribbon diagrams of the mean AbrBN53 structure calculated from the 20 lowest energy structures.
Figure 3: Electrostatic surface potential, chemical shift mapping, and a model of AbrBN53 binding to DNA.
Figure 4
Figure 5: Subunit mixing experiment between equimolar amounts of AbrB and the AbrB R23S mutant.

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Acknowledgements

We thank D. Schaak, J. Osterhout, and R. Cunningham for helpful discussions. We are also indebted to K. Xu for providing purified wild type AbrB protein for the initial phases of this study. N. Skelton generously provided analytical scripts and insightful discussion. This work was supported by grants to J.C. from NIH and the Army Research Office.

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  1. John Cavanagh

    Present address: Department of Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, North Carolina, 27695, USA

Authors and Affiliations

  1. Department of Chemistry, Purdue University, 1393 Brown Building, West Lafayette, 47907, Indiana, USA

    Jeffrey L. Vaughn & John Cavanagh

  2. Department of Biological Sciences, State University of New York/Albany, 1400 Washington Ave, Albany , 12222, New York, USA

    Jeffrey L. Vaughn

  3. Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla , 92037, California, USA

    Victoria Feher

  4. Department of Biochemistry and Molecular Biology, Biomedical Mass Spectrometry, and Functional Proteomics Facility, Mayo Clinic/Foundation, Rochester, 55905, Minnesota, USA

    Stephen Naylor

  5. Department of Oral and Craniofacial Biological Sciences, University of Maryland Dental School, 666 W. Baltimore Street , Baltimore, 21201, Maryland, USA

    Mark A. Strauch

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Correspondence to John Cavanagh.

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Vaughn, J., Feher, V., Naylor, S. et al. Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB. Nat Struct Mol Biol 7, 1139–1146 (2000). https://doi.org/10.1038/81999

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