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Protein Science (2007), 16:1676-1688. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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The solution structure of ParD, the antidote of the ParDE toxin–antitoxin module, provides the structural basis for DNA and toxin binding

Monika Oberer1, Klaus Zangger2, Karl Gruber1, and Walter Keller1

1 Institut für Chemie, Arbeitsgruppe Strukturbiologie, Karl-Franzens-Universität Graz, A-8010 Graz, Austria
2 Bereich Organische und Bioorganische Chemie, Karl-Franzens-Universität Graz, A-8010 Graz, Austria

(RECEIVED November 26, 2006; FINAL REVISION May 16, 2007; ACCEPTED May 16, 2007)

ParD is the antidote of the plasmid-encoded toxin–antitoxin (TA) system ParD–ParE. These modules rely on differential stabilities of a highly expressed but labile antidote and a stable toxin expressed from one operon. Consequently, loss of the coding plasmid results in loss of the protective antidote and poisoning of the cell. The antidote protein usually also exhibits an autoregulatory function of the operon. In this paper, we present the solution structure of ParD. The repressor activity of ParD is mediated by the N-terminal half of the protein, which adopts a ribbon-helix-helix (RHH) fold. The C-terminal half of the protein is unstructured in the absence of its cognate binding partner ParE. Based on homology with other RHH proteins, we present a model of the ParD–DNA interaction, with the antiparallel beta-strand being inserted into the major groove of DNA. The fusion of the N-terminal DNA-binding RHH motif to the toxin-binding unstructured C-terminal domain is discussed in its evolutionary context.

Keywords: NMR spectroscopy; ribbon-helix-helix; intermonomer NOEs; homodimeric protein; toxin–antitoxin systems; bacterial programmed cell death


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