Summary information and primary citation
- PDB-id
-
3w3c;
DSSR-derived features in text and
JSON formats
- Class
- transcription-DNA
- Method
- X-ray (2.431 Å)
- Summary
- Crystal structure of virb core domain complexed with
the cis-acting site upstream icsb promoter
- Reference
-
Gao XP, Zou TT, Mu ZX, Qin B, Yang J, Waltersperger S,
Wang MT, Cui S, Jin Q (2013): "Structural
insights into VirB-DNA complexes reveal mechanism of
transcriptional activation of virulence genes."
Nucleic Acids Res., 41,
10529-10541. doi: 10.1093/nar/gkt748.
- Abstract
- VirB activates transcription of virulence genes in
Shigella flexneri by alleviating heat-stable
nucleoid-structuring protein-mediated promoter repression.
VirB is unrelated to the conventional transcriptional
regulators, but homologous to the plasmid partitioning
proteins. We determined the crystal structures of VirB HTH
domain bound by the cis-acting site containing the inverted
repeat, revealing that the VirB-DNA complex is related to
ParB-ParS-like complexes, presenting an example that a
ParB-like protein acts exclusively in transcriptional
regulation. The HTH domain of VirB docks DNA major groove
and provides multiple contacts to backbone and bases, in
which the only specific base readout is mediated by R167.
VirB only recognizes one half site of the inverted repeats
containing the most matches to the consensus for VirB
binding. The binding of VirB induces DNA conformational
changes and introduces a bend at an invariant A-tract
segment in the cis-acting site, suggesting a role of DNA
remodeling. VirB exhibits positive cooperativity in DNA
binding that is contributed by the C-terminal domain
facilitating VirB oligomerization. The isolated HTH domain
only confers partial DNA specificity. Additional
determinants for sequence specificity may reside in N- or
C-terminal domains. Collectively, our findings support and
extend a previously proposed model for relieving
heat-stable nucleoid-structuring protein-mediated
repression by VirB.
