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J Bacteriol. 2014 Jun;196(12):2131-42. doi: 10.1128/JB.01486-13. Epub 2014 Feb 28.

Structure of bacterial transcription factor SpoIIID and evidence for a novel mode of DNA binding.

Author information

1
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
2
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA yanh@msu.edu kroos@msu.edu.

Abstract

SpoIIID is evolutionarily conserved in endospore-forming bacteria, and it activates or represses many genes during sporulation of Bacillus subtilis. An SpoIIID monomer binds DNA with high affinity and moderate sequence specificity. In addition to a predicted helix-turn-helix motif, SpoIIID has a C-terminal basic region that contributes to DNA binding. The nuclear magnetic resonance (NMR) solution structure of SpoIIID in complex with DNA revealed that SpoIIID does indeed have a helix-turn-helix domain and that it has a novel C-terminal helical extension. Residues in both of these regions interact with DNA, based on the NMR data and on the effects on DNA binding in vitro of SpoIIID with single-alanine substitutions. These data, as well as sequence conservation in SpoIIID binding sites, were used for information-driven docking to model the SpoIIID-DNA complex. The modeling resulted in a single cluster of models in which the recognition helix of the helix-turn-helix domain interacts with the major groove of DNA, as expected. Interestingly, the C-terminal extension, which includes two helices connected by a kink, interacts with the adjacent minor groove of DNA in the models. This predicted novel mode of binding is proposed to explain how a monomer of SpoIIID achieves high-affinity DNA binding. Since SpoIIID is conserved only in endospore-forming bacteria, which include important pathogenic Bacilli and Clostridia, whose ability to sporulate contributes to their environmental persistence, the interaction of the C-terminal extension of SpoIIID with DNA is a potential target for development of sporulation inhibitors.

PMID:
24584501
PMCID:
PMC4054184
DOI:
10.1128/JB.01486-13
[Indexed for MEDLINE]
Free PMC Article

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