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Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.

McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale GG - Nucleic Acids Res. (2011)

Bottom Line: The molecular recognition of promoter sequences by such transcriptional regulators is poorly understood, in part because the DNA sequence motifs do not conform to a well-defined symmetry.The structure reveals how two different symmetries within the operator are simultaneously recognized by the homo-dimeric protein, underpinned by a conformational change in one of the protein subunits.The recognition of two different DNA symmetries through movement of a flexible loop in one of the protein subunits may represent a general mechanism for the recognition of pseudo-symmetric DNA sequences.

View Article: PubMed Central - PubMed

Affiliation: Biomolecular Structure Group, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, UK.

ABSTRACT
The controller protein C.Esp1396I regulates the timing of gene expression of the restriction-modification (RM) genes of the RM system Esp1396I. The molecular recognition of promoter sequences by such transcriptional regulators is poorly understood, in part because the DNA sequence motifs do not conform to a well-defined symmetry. We report here the crystal structure of the controller protein bound to a DNA operator site. The structure reveals how two different symmetries within the operator are simultaneously recognized by the homo-dimeric protein, underpinned by a conformational change in one of the protein subunits. The recognition of two different DNA symmetries through movement of a flexible loop in one of the protein subunits may represent a general mechanism for the recognition of pseudo-symmetric DNA sequences.

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Comparison of the interactions made by the flexible loop region in chains A and B of the 19-mer OL complex structure. The hydrogen bond interactions made by the flexible loop regions in chains A and B (a and b, respectively) are shown as black dashes. Residues involved in stabilizing the loop region are represented as thin lines. Water molecules are represented by green spheres.
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gkr1250-F5: Comparison of the interactions made by the flexible loop region in chains A and B of the 19-mer OL complex structure. The hydrogen bond interactions made by the flexible loop regions in chains A and B (a and b, respectively) are shown as black dashes. Residues involved in stabilizing the loop region are represented as thin lines. Water molecules are represented by green spheres.

Mentions: Figure 5 shows both loop conformations with respect to the DNA, and the atoms involved (see also Supplementary Figure S5). The side-chain of N44 in the major loop (Figure 5a) points towards the core of the protein and the terminal carbonyl and amino groups, are stabilized directly through interactions with the backbone amino group of S7 and the γ-hydroxyl of S10. The δ-amino of N44 and the backbone carbonyl of S7 also coordinate a water. These interactions provide stability for the major loop conformation. In the minor loop conformation (Figure 5b) the N44 rotates ∼180° about the backbone and the side-chain points towards the DNA backbone. The δ-amino of N44, the η-amino of R43 and the phosphate oxygen of G5 coordinate a water that stabilizes the N44 sidechain.Figure 5.


Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.

McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale GG - Nucleic Acids Res. (2011)

Comparison of the interactions made by the flexible loop region in chains A and B of the 19-mer OL complex structure. The hydrogen bond interactions made by the flexible loop regions in chains A and B (a and b, respectively) are shown as black dashes. Residues involved in stabilizing the loop region are represented as thin lines. Water molecules are represented by green spheres.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351150&req=5

gkr1250-F5: Comparison of the interactions made by the flexible loop region in chains A and B of the 19-mer OL complex structure. The hydrogen bond interactions made by the flexible loop regions in chains A and B (a and b, respectively) are shown as black dashes. Residues involved in stabilizing the loop region are represented as thin lines. Water molecules are represented by green spheres.
Mentions: Figure 5 shows both loop conformations with respect to the DNA, and the atoms involved (see also Supplementary Figure S5). The side-chain of N44 in the major loop (Figure 5a) points towards the core of the protein and the terminal carbonyl and amino groups, are stabilized directly through interactions with the backbone amino group of S7 and the γ-hydroxyl of S10. The δ-amino of N44 and the backbone carbonyl of S7 also coordinate a water. These interactions provide stability for the major loop conformation. In the minor loop conformation (Figure 5b) the N44 rotates ∼180° about the backbone and the side-chain points towards the DNA backbone. The δ-amino of N44, the η-amino of R43 and the phosphate oxygen of G5 coordinate a water that stabilizes the N44 sidechain.Figure 5.

Bottom Line: The molecular recognition of promoter sequences by such transcriptional regulators is poorly understood, in part because the DNA sequence motifs do not conform to a well-defined symmetry.The structure reveals how two different symmetries within the operator are simultaneously recognized by the homo-dimeric protein, underpinned by a conformational change in one of the protein subunits.The recognition of two different DNA symmetries through movement of a flexible loop in one of the protein subunits may represent a general mechanism for the recognition of pseudo-symmetric DNA sequences.

View Article: PubMed Central - PubMed

Affiliation: Biomolecular Structure Group, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, UK.

ABSTRACT
The controller protein C.Esp1396I regulates the timing of gene expression of the restriction-modification (RM) genes of the RM system Esp1396I. The molecular recognition of promoter sequences by such transcriptional regulators is poorly understood, in part because the DNA sequence motifs do not conform to a well-defined symmetry. We report here the crystal structure of the controller protein bound to a DNA operator site. The structure reveals how two different symmetries within the operator are simultaneously recognized by the homo-dimeric protein, underpinned by a conformational change in one of the protein subunits. The recognition of two different DNA symmetries through movement of a flexible loop in one of the protein subunits may represent a general mechanism for the recognition of pseudo-symmetric DNA sequences.

Show MeSH