2BNW

Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct DNA heptad repeats

Summary for 2BNW

• Entry DOI: 10.2210/pdb2bnw/pdb
• Related: 1IRQ 2BNZ 2CAX
• Descriptor: ORF OMEGA, 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3', 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3', ... (4 entities in total)
• Functional Keywords: dna-binding-regulatory protein complex, ribbon-helix-helix, rhh, metj/arc superfamily, cooperative dna binding, inverted repeats, dna heptad, inc18 family, dna-binding regulatory protein, dna-binding/regulatory protein
• Biological source: STREPTOCOCCUS PYOGENES (STREPTOCOCCUS); More
• Total number of polymer chains: 8
• Total formula weight: 46609.28

Authors

Weihofen, W.A.,Cicek, A.,Pratto, F.,Alonso, J.C.,Saenger, W. (deposition date: 2005-04-05, release date: 2006-03-15, Last modification date: 2023-12-13)

Primary citation

Weihofen, W.A.,Cicek, A.,Pratto, F.,Alonso, J.C.,Saenger, W.
Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription.
Nucleic Acids Res., 34:1450-, 2006

PubMed Abstract: 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.

PubMed: 16528102
DOI: 10.1093/NAR/GKL015

Experimental method

X-RAY DIFFRACTION (2.45 Å)