2BNZ: Structural Basis For Cooperative Binding Of Ribbon-helix- Helix Omega Repressor To Inverted Dna Heptad Repeats

Repressor omega regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. omega belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel beta-sheet for DNA major groove binding. Homodimeric omega2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5'-(A)/(T)ATCAC(A)/(T)-3', symbolized by -->) in palindromic inverted, converging (--><--) or diverging (<---->) orientation and also, unique to omega2 and contrasting other RHH2 repressors, to non-palindromic direct (-->-->) repeats. Here we investigate with crystal structures how omega2 binds specifically to heptads in minimal operators with (-->-->) and (--><--) repeats. Since the pseudo-2-fold axis relating the monomers in omega(2) passes the central C-G base pair of each heptad with approximately 0.3 A downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (-->-->), approximately 0.6 A shorter in (--><--) but would be approximately 0.6 A longer in (<---->). These variations grade interactions between adjacent omega2 and explain modulations in cooperative binding affinity of omega2 to operators with different heptad orientations.
PDB ID: 2BNZDownload
MMDB ID: 74533
PDB Deposition Date: 2005/4/6
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 2BNZ: octameric; determined by author and by software (PISA)
Molecular Components in 2BNZ
Label Count Molecule
Proteins (4 molecules)
ORF Omega
Molecule annotation
Nucleotides(2 molecules)
5'-d(*gp*ap*ap*tp*cp*ap*cp*ap*ap*gp *tp*gp*ap*tp*tp*ap*gp*c)-3'
Molecule annotation
5'-d(*cp*tp*ap*ap*tp*cp*ap*cp*tp*tp *gp*tp*gp*ap*tp*tp*cp*g)-3'
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB