The solution structure of ParD, the antidote of the ParDE toxin–antitoxin module, provides the structural basis for DNA and toxin binding

Abstract

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 b-strand being inserted into the major groove of DNA. The fusion of the N-terminal DNAbinding RHH motif to the toxin-binding unstructured C-terminal domain is discussed in its evolutionary context.

Influence of Operator Site Geometry on Transcriptional Control by the YefM-YoeB Toxin-Antitoxin Complex

“…The complex interacts discontinuously with the DNA, with alternating stretches of occupation and absence (10). The tertiary structures of numerous antitoxin proteins have been elucidated recently, either as part of a complex with the cognate toxin and/or in the unbound form or in association with operator site DNA (19,20,22,24,28,31,32,35,36,43,53). These structures have revealed significant diversity in the folds that antitoxins use to bind to their regulatory sites.…”

“…The CcdA dimer possesses a ribbon-helix-helix (RHH) structure in which basic residues located in antiparallel ␤-strands interact with numerous 6-bp palindromic sequences as mentioned above (10,32). Similarly, the FitA, RelB, and ParD antitoxins are RHH dimers that bind their cognate operator sites (28,35,43), as is the protein which is a discrete factor that represses transcription of the ε TA complex (40). An archaeal RelB homologue lacks the RHH fold found in bacterial RelB proteins but instead was proposed to recognize DNA via a cluster of basic residues at its N-terminal end (53).…”

Structure and Proposed Activity of a Member of the VapBC Family of Toxin-Antitoxin Systems

“…Five TA families have been identified on the M. tuberculosis chromosome: one member from the higBA family, two from parDE (15), three from relBE (16), nine from mazEF (17), and 23 from vapBC (5,14). The E. coli MazEF and the archaeal RelBE systems have been extensively studied.…”

The crystal structure of the Rv0301‐Rv0300 VapBC‐3 toxin—antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA‐binding site

“…2 The first toxin structure to be determined was the E. coli F plasmid CcdB toxin. 3 The structures of many toxins, antitoxins, and TA complexes have been determined since, including E. coli plasmid R1 Kid toxin, 4 E. coli MazE-MazF TA complex, 5 broad-hostrange low-copy-number plasmid pSM19035 from Streptococcus pyogenes e 2 f 2 TA complex, 6 E. coli YoeB toxin and YefM2-YoeB TA complex, 7 archaeal Pyrococcus horikoshii aRelE-aRelB TA complex, 8 Neisseria gonorrhoeae FitAB TA complex, 9 solution structure of the broad host range low-copy-number plasmid pRK2/RP4 ParD antitoxin, 10 Mycobacterium tuberculosis (Mtb)…”