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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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Schematic representation of nucleoprotein interactions. (a) Residues Arg35, Thr36 and Arg46 are involved in direct readout of the DNA sequence. (b) Overview of protein–DNA interactions. Phosphate groups are represented as circles, and those interacting with the protein are coloured according to the subunit contacted. Interactions between chain A and the DNA are highlighted in blue and interactions between chain B and DNA are highlighted in green (for further details, see Supplementary Figures S7 and S8).
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gkr1250-F9: Schematic representation of nucleoprotein interactions. (a) Residues Arg35, Thr36 and Arg46 are involved in direct readout of the DNA sequence. (b) Overview of protein–DNA interactions. Phosphate groups are represented as circles, and those interacting with the protein are coloured according to the subunit contacted. Interactions between chain A and the DNA are highlighted in blue and interactions between chain B and DNA are highlighted in green (for further details, see Supplementary Figures S7 and S8).

Mentions: The tetrameric complex structure suggested a possible role for Y37 and S52 of each subunit in the dimer in compressing the minor groove at the TATA sequences by binding to the phosphate backbone of the DNA on either side (11). These interactions are seen much more clearly in the OL complex structure, with additional backbone contacts being made by N47 (Figure 7). For each subunit, the hydroxyl groups of Y37 and S52 interact with the same phosphate group of the DNA (5′ of nucleotide 13 in both DNA strands) and the amino group of N47 interacts with the phosphate 5′ of nucleotide 12. The serine in chain B has a dual conformation (both conformations were refined with 50% occupancy), but both conformations interact with the same phosphate group. These interactions cause the minor groove to be compressed and the DNA to be bent. In addition, there are interactions of the side-chains of residues R17, N24, S39 and R43 with phosphate groups at either end of the DNA (Figure 9 and Supplementary Figures S7 and S8), which further stabilize the bent DNA conformation. The interactions of the negatively charged phosphate groups with the positively charged guanidinium groups of R17 and R43 will be particularly strong, and should make an important contribution to the overall binding energy.Figure 9.


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)

Schematic representation of nucleoprotein interactions. (a) Residues Arg35, Thr36 and Arg46 are involved in direct readout of the DNA sequence. (b) Overview of protein–DNA interactions. Phosphate groups are represented as circles, and those interacting with the protein are coloured according to the subunit contacted. Interactions between chain A and the DNA are highlighted in blue and interactions between chain B and DNA are highlighted in green (for further details, see Supplementary Figures S7 and S8).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkr1250-F9: Schematic representation of nucleoprotein interactions. (a) Residues Arg35, Thr36 and Arg46 are involved in direct readout of the DNA sequence. (b) Overview of protein–DNA interactions. Phosphate groups are represented as circles, and those interacting with the protein are coloured according to the subunit contacted. Interactions between chain A and the DNA are highlighted in blue and interactions between chain B and DNA are highlighted in green (for further details, see Supplementary Figures S7 and S8).
Mentions: The tetrameric complex structure suggested a possible role for Y37 and S52 of each subunit in the dimer in compressing the minor groove at the TATA sequences by binding to the phosphate backbone of the DNA on either side (11). These interactions are seen much more clearly in the OL complex structure, with additional backbone contacts being made by N47 (Figure 7). For each subunit, the hydroxyl groups of Y37 and S52 interact with the same phosphate group of the DNA (5′ of nucleotide 13 in both DNA strands) and the amino group of N47 interacts with the phosphate 5′ of nucleotide 12. The serine in chain B has a dual conformation (both conformations were refined with 50% occupancy), but both conformations interact with the same phosphate group. These interactions cause the minor groove to be compressed and the DNA to be bent. In addition, there are interactions of the side-chains of residues R17, N24, S39 and R43 with phosphate groups at either end of the DNA (Figure 9 and Supplementary Figures S7 and S8), which further stabilize the bent DNA conformation. The interactions of the negatively charged phosphate groups with the positively charged guanidinium groups of R17 and R43 will be particularly strong, and should make an important contribution to the overall binding energy.Figure 9.

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