3W3C

Crystal structure of VirB core domain complexed with the cis-acting site upstream icsb promoter

3W3C の概要

• エントリーDOI: 10.2210/pdb3w3c/pdb
• 関連するPDBエントリー: 1zx4 2ntz 3mkz 3VWB 3W2A
• 分子名称: Virulence regulon transcriptional activator VirB, DNA (26-MER), ... (4 entities in total)
• 機能のキーワード: hth dna binding motif, protein-dna complex, parb box-a like sequence, parb like fold, transcriptional activator, sequence specific dsdna binding, transcription-dna complex, transcription/dna
• 由来する生物種: Shigella flexneri 2a; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 32227.06

構造登録者

Gao, X.P.,Waltersperger, S.,Wang, M.T.,Cui, S. (登録日: 2012-12-19, 公開日: 2013-09-04, 最終更新日: 2023-11-08)

主引用文献

Gao, X.P.,Zou, T.T.,Mu, Z.X.,Qin, B.,Yang, J.,Waltersperger, S.,Wang, M.T.,Cui, S.,Jin, Q.
Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes
Nucleic Acids Res., 41:10529-10541, 2013

PubMed 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.

PubMed: 23985969
DOI: 10.1093/nar/gkt748

実験手法

X-RAY DIFFRACTION (2.431 Å)