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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 between the two half sites in the 19-mer OL complex structure. (a) Monomers A and B (blue and green, respectively) were superimposed with RMSD = 0.34 Å (222 main chain atoms). The DNA bases are offset by approximately half a base pair. Bases involved in direct readout are shown as thick lines. The half base pair shift is compensated for through the flexibility of the loop region, permitting recognition of the GTC bases. (b) Residues 13–15 of chain C (blue) were superimposed upon residues 14–16 of chain D (green) (RMSD = 0.54 Å over 61 backbone atoms). Hydrogen bonds are represented by dashed lines.
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gkr1250-F6: Comparison between the two half sites in the 19-mer OL complex structure. (a) Monomers A and B (blue and green, respectively) were superimposed with RMSD = 0.34 Å (222 main chain atoms). The DNA bases are offset by approximately half a base pair. Bases involved in direct readout are shown as thick lines. The half base pair shift is compensated for through the flexibility of the loop region, permitting recognition of the GTC bases. (b) Residues 13–15 of chain C (blue) were superimposed upon residues 14–16 of chain D (green) (RMSD = 0.54 Å over 61 backbone atoms). Hydrogen bonds are represented by dashed lines.

Mentions: Figure 6a shows a superposition of subunits A and B by a rotation about the dyad axis that relates them. The overall backbone structure of the two subunits is very similar, with the only notable difference occurring in the flexible loop region. The GTC motif recognized the by amino acid side-chains of T36 and R46 shifts by approximately half a base pair relative to the protein. The flexible loop is able to accommodate this half base pair shift, permitting recognition of the GTC by monomer B. In an alternative view, if the GTC bases that are recognized by each subunit (one in each half-site) are superimposed (Figure 6b), the protein rotates by ∼30° around the helix axis of the DNA.Figure 6.


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 between the two half sites in the 19-mer OL complex structure. (a) Monomers A and B (blue and green, respectively) were superimposed with RMSD = 0.34 Å (222 main chain atoms). The DNA bases are offset by approximately half a base pair. Bases involved in direct readout are shown as thick lines. The half base pair shift is compensated for through the flexibility of the loop region, permitting recognition of the GTC bases. (b) Residues 13–15 of chain C (blue) were superimposed upon residues 14–16 of chain D (green) (RMSD = 0.54 Å over 61 backbone atoms). Hydrogen bonds are represented by dashed lines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkr1250-F6: Comparison between the two half sites in the 19-mer OL complex structure. (a) Monomers A and B (blue and green, respectively) were superimposed with RMSD = 0.34 Å (222 main chain atoms). The DNA bases are offset by approximately half a base pair. Bases involved in direct readout are shown as thick lines. The half base pair shift is compensated for through the flexibility of the loop region, permitting recognition of the GTC bases. (b) Residues 13–15 of chain C (blue) were superimposed upon residues 14–16 of chain D (green) (RMSD = 0.54 Å over 61 backbone atoms). Hydrogen bonds are represented by dashed lines.
Mentions: Figure 6a shows a superposition of subunits A and B by a rotation about the dyad axis that relates them. The overall backbone structure of the two subunits is very similar, with the only notable difference occurring in the flexible loop region. The GTC motif recognized the by amino acid side-chains of T36 and R46 shifts by approximately half a base pair relative to the protein. The flexible loop is able to accommodate this half base pair shift, permitting recognition of the GTC by monomer B. In an alternative view, if the GTC bases that are recognized by each subunit (one in each half-site) are superimposed (Figure 6b), the protein rotates by ∼30° around the helix axis of the DNA.Figure 6.

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