3UFD

C.Esp1396I bound to its highest affinity operator site OM

Summary for 3UFD

• Entry DOI: 10.2210/pdb3ufd/pdb
• Related: 3CLC 3FYA 3G5G 3S8Q
• Descriptor: Regulatory protein, DNA (5'-D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3'), DNA (5'-D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3'), ... (5 entities in total)
• Functional Keywords: helix-turn-helix, bacterial gene regulatory protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Enterobacter sp. RFL1396
• Total number of polymer chains: 8
• Total formula weight: 61415.34

Authors

Ball, N.J.,McGeehan, J.E.,Streeter, S.D.,Thresh, S.-J.,Kneale, G.G. (deposition date: 2011-11-01, release date: 2012-07-11, Last modification date: 2024-02-28)

Primary citation

Ball, N.J.,McGeehan, J.E.,Streeter, S.D.,Thresh, S.J.,Kneale, G.G.
The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
Nucleic Acids Res., 40:10532-10542, 2012

PubMed Abstract: Controller (C) proteins regulate the expression of restriction-modification (RM) genes in a wide variety of RM systems. However, the RM system Esp1396I is of particular interest as the C protein regulates both the restriction endonuclease (R) gene and the methyltransferase (M) gene. The mechanism of this finely tuned genetic switch depends on differential binding affinities for the promoters controlling the R and M genes, which in turn depends on differential DNA sequence recognition and the ability to recognize dual symmetries. We report here the crystal structure of the C protein bound to the M promoter, and compare the binding affinities for each operator sequence by surface plasmon resonance. Comparison of the structure of the transcriptional repression complex at the M promoter with that of the transcriptional activation complex at the R promoter shows how subtle changes in protein-DNA interactions, underpinned by small conformational changes in the protein, can explain the molecular basis of differential regulation of gene expression.

PubMed: 22941636
DOI: 10.1093/nar/gks718

Experimental method

X-RAY DIFFRACTION (2.8 Å)