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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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Related in: MedlinePlus

Non-specific DNA contacts stabilize the complex and the compression of the minor groove. Chains A–D are coloured blue, green, beige and pink, respectively. Hydrogen bonds are represented by dashed lines. The nucleoprotein complex is stabilized by non-specific interactions between amino acids (e.g. R43; inset left and right) and the phosphodiester backbone of DNA. The minor groove is compressed at the TATA sequence, which results in the DNA being significantly bent. Y37, N47 and S52 from both monomers are involved in stabilizing the bend (inset centre).
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gkr1250-F7: Non-specific DNA contacts stabilize the complex and the compression of the minor groove. Chains A–D are coloured blue, green, beige and pink, respectively. Hydrogen bonds are represented by dashed lines. The nucleoprotein complex is stabilized by non-specific interactions between amino acids (e.g. R43; inset left and right) and the phosphodiester backbone of DNA. The minor groove is compressed at the TATA sequence, which results in the DNA being significantly bent. Y37, N47 and S52 from both monomers are involved in stabilizing the bend (inset centre).

Mentions: Analysis of the OL DNA structure in the complex was performed using CURVES (22). The minor groove at the TATA site is compressed (from ∼7 Å to ∼2 Å), which leads to the DNA being significantly bent about this sequence, as shown in Figure 7. The overall bend of the DNA duplex is ∼40°. From circular permutation assays, it is clear that the DNA is not intrinsically bent; rather, the bending is induced when the C-protein binds to its operator, i.e. the sequence of the operator DNA is one that can readily be deformed when the C-protein binds (11,14). DNA bending around the TATA site permits a form of indirect readout. The bend in the DNA at the TATA site is accompanied by deviations in the base pair and step parameters (Figure 8 and Supplementary Figure S6). The parameters for the OL sequence show values that are typical of TATA sequences (23) except for the roll parameter, which is closer to standard B-form DNA. The twist values for the two thymines differ significantly from the standard B-form values, suggesting that the DNA bending can be achieved by partially unstacking the TATA bases.Figure 7.


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)

Non-specific DNA contacts stabilize the complex and the compression of the minor groove. Chains A–D are coloured blue, green, beige and pink, respectively. Hydrogen bonds are represented by dashed lines. The nucleoprotein complex is stabilized by non-specific interactions between amino acids (e.g. R43; inset left and right) and the phosphodiester backbone of DNA. The minor groove is compressed at the TATA sequence, which results in the DNA being significantly bent. Y37, N47 and S52 from both monomers are involved in stabilizing the bend (inset centre).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkr1250-F7: Non-specific DNA contacts stabilize the complex and the compression of the minor groove. Chains A–D are coloured blue, green, beige and pink, respectively. Hydrogen bonds are represented by dashed lines. The nucleoprotein complex is stabilized by non-specific interactions between amino acids (e.g. R43; inset left and right) and the phosphodiester backbone of DNA. The minor groove is compressed at the TATA sequence, which results in the DNA being significantly bent. Y37, N47 and S52 from both monomers are involved in stabilizing the bend (inset centre).
Mentions: Analysis of the OL DNA structure in the complex was performed using CURVES (22). The minor groove at the TATA site is compressed (from ∼7 Å to ∼2 Å), which leads to the DNA being significantly bent about this sequence, as shown in Figure 7. The overall bend of the DNA duplex is ∼40°. From circular permutation assays, it is clear that the DNA is not intrinsically bent; rather, the bending is induced when the C-protein binds to its operator, i.e. the sequence of the operator DNA is one that can readily be deformed when the C-protein binds (11,14). DNA bending around the TATA site permits a form of indirect readout. The bend in the DNA at the TATA site is accompanied by deviations in the base pair and step parameters (Figure 8 and Supplementary Figure S6). The parameters for the OL sequence show values that are typical of TATA sequences (23) except for the roll parameter, which is closer to standard B-form DNA. The twist values for the two thymines differ significantly from the standard B-form values, suggesting that the DNA bending can be achieved by partially unstacking the TATA bases.Figure 7.

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
Related in: MedlinePlus