2CAX

STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS

Summary for 2CAX

• Entry DOI: 10.2210/pdb2cax/pdb
• Related: 1IRQ 2BNW 2BNZ
• Descriptor: ORF OMEGA, 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*G)-3', 5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)-3', ... (6 entities in total)
• Functional Keywords: transcriptional repressor, inc18 family of plasmids, rhh, metj/arc superfamily, cooperative dna binding, dna heptad 5'- a/t atcac a/t -3', plasmid maintenance, dna- binding, regulatory protein
• Biological source: STREPTOCOCCUS PYOGENES; More
• Total number of polymer chains: 8
• Total formula weight: 46031.90

Authors

Weihofen, W.A.,Cicek, A.,Pratto, F.,Alonso, J.C.,Saenger, W. (deposition date: 2005-12-23, release date: 2006-03-15, Last modification date: 2024-05-08)

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 (2.9 Å)