PDBsum entry 3w3c

Transcription/DNA

PDB id: 3w3c

Contents

Protein chain

116 a.a.

DNA/RNA

Waters ×70

PDB id:

3w3c

Name:

Transcription/DNA

Title:

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

Structure:

Virulence regulon transcriptional activator virb. Chain: a. Fragment: unp residues 129-250. Synonym: cell invasion regulator inve. Engineered: yes. DNA (26-mer). Chain: b. Engineered: yes. DNA (26-mer).

Source:

Shigella flexneri 2a. Organism_taxid: 42897. Strain: 301. Gene: virb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA

Resolution:

2.43Å R-factor: 0.265 R-free: 0.280

Authors:

X.P.Gao,S.Waltersperger,M.T.Wang,S.Cui

Key ref:

X.Gao et al. (2013). Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes. Nucleic Acids Res, 41, 10529-10541. PubMed id: 23985969 DOI: 10.1093/nar/gkt748

Date:

19-Dec-12 Release date: 04-Sep-13

Protein chain

P0A247  (VIRB_SHIFL) -  Virulence regulon transcriptional activator VirB from Shigella flexneri

Seq: 309 a.a.

Struc: 116 a.a.

DNA/RNA chains

T-T-T-G-T-G-G-G-A-T-T-T-C-A-T-G-A-T-G-A-A-A-C-G-A-G 26 bases

A-A-A-C-T-C-G-T-T-T-C-A-T-C-A-T-G-A-A-A-T-C-C-C-A-C 26 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/nar/gkt748

Nucleic Acids Res 41:10529-10541 (2013)

PubMed id: 23985969

Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes.

X.Gao, T.Zou, Z.Mu, B.Qin, J.Yang, S.Waltersperger, M.Wang, S.Cui, Q.Jin.

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.