## 3 CcdA-CcdB: Transcriptional Repression of a DNA Gyrase Poison  
The CcdA-CcdB TA complex first was identified as a maintenance system encoded by the F plasmid in _Escherichia coli_[33]. Genes for homologous complexes are distributed widely on both bacterial plasmids and chromosomes, although are less common than certain other TA loci [34]. DNA gyrase is an essential type II topoisomerase that introduces negative supercoils into bacterial DNA. The CcdB toxin poisons covalent gyrase-DNA complexes both by entrapping the gyrase cleavage complex and by inhibiting the enzyme's catalytic reactions [28,35]. The CcdA antitoxin sequesters CedB thereby blocking interference with gyrase [36].  
The _ccdA-ccdB_ genes form an operon that is autoregulated at the transcriptional level. Although CcdA alone binds the _ccdA-ccdB_ promoter-operator region _in vitro_, repression _in vivo_ is mediated by the CcdA-CcdB complex [37, 38, 39, 40]. The two-protein complex also binds DNA more avidly and with higher specificity _in vitro_ than does CcdA alone [41,42]. CcdB does not bind DNA [37]. The N-terminal region of CcdA adopts a dimeric, ribbon-helix-helix (RHH) fold that is characteristic of a broad family of prokaryotic transcriptional repressors that regulate a variety of cellular processes (Figure 2A) [43]. Like other RHH proteins, the CcdA antitoxin binds DNA by insertion of a pair of positively charged, antiparallel \(\beta\)-strands into the major groove. The C-terminal region of CcdA is highly mobile but is stabilized by interaction with CcdB which in part may be due to obscuring of the site recognized on CcdA by the Lon protease [44]. CcdA recognizes a 6-bp palindrome downstream of the -10 promoter element for the _ccdA-ccdB_ operon (Figure 3). This hexamer is thought to be a nucleation site for assembly of an extended superstructure in which multiple CcdA-CcdB complexes spiral around \(\sim\)120-bp of DNA that encompasses the promoter-operator and the 5' end of the _ccdA_ gene [39, 40, 41]. The biological purpose of this higher order nucleoprotein complex is uncertain, but may permit a gradated transition of _ccdA-ccdB_ expression dependent on the extent of spreading of the CcdA-CcdB complex from the nucleation point.  
**Figure 2.** Tertiary structures of selected antitoxins and TA complexes. (**A**) solution structure of CcdA antitoxin [44]. The structure comprises a dimeric, N-terminal ribbon-helix-helix (RHH) fold (red and blue) that binds DNA connected to a pair of C-terminal extensions (orange) that become structured upon interaction with the CcdB toxin [44]. The antiparallel \(\beta\)-strands in the RHH fold that insert into the DNA major groove are highlighted in blue. (**B**) crystal structure of the YefM-YoeB complex [45]. The YefM antitoxin dimer and YoeB toxin monomer are coloured in blue and magenta, respectively. Conserved arginine residues in the N-terminal segment of YefM that are involved in operator recognition [46] are highlighted in yellow. (**C**) crystal structure of the FitA-FitB-DNA complex [47]. FitA and FitB are shown in magenta and green, respectively. The structure comprises four FitA-FitB heterodimers assembled on a 36-bp DNA segment (orange) from the regulatory region upstream of _fitA-fitB_. (**D**) crystal structure of the MsqA antitoxin [48]. Monomers within the dimeric structure are coloured green and blue. Zinc ions involved in maintaining MsqA structural stability are shown as red spheres. (**E**) crystal structure of the VapB2-VapC2 complex of _Rickettsia felis_[49]. The structure consists of four VapC toxin molecules (green) and four antitoxin monomers (magenta) which form a tetramer of heterodimers assembled on a 26-bp DNA segment. Images constructed using the Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Molecular Biology Toolkit [50].