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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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The C.Esp1396I OL nucleoprotein complex structure. The asymmetric unit of the crystal contains a C.Esp1396I dimer (chains A and B; blue and green, respectively) bound to DNA (chains C and D; beige and pink, respectively). The DNA duplex consists of 18 bp with a 5′ overhang on each strand.
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gkr1250-F3: The C.Esp1396I OL nucleoprotein complex structure. The asymmetric unit of the crystal contains a C.Esp1396I dimer (chains A and B; blue and green, respectively) bound to DNA (chains C and D; beige and pink, respectively). The DNA duplex consists of 18 bp with a 5′ overhang on each strand.

Mentions: One complex, consisting of a C.Esp1396I dimer bound to a DNA duplex (Figure 3), is present in the asymmetric unit and the structure refined to 2.1 Å with a final R/Rfree of 16.8/22.4% (Table 1). Iterative refinement was carried out using Refmac (19) with TLS restraints enabled. All of the DNA bases are clearly resolved, as are all except a few amino acid residues at the N and C termini of each protein subunit. In addition, a total of 314 solvent molecules could be located, including a number of water molecules mediating protein–DNA interactions.Figure 3.


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)

The C.Esp1396I OL nucleoprotein complex structure. The asymmetric unit of the crystal contains a C.Esp1396I dimer (chains A and B; blue and green, respectively) bound to DNA (chains C and D; beige and pink, respectively). The DNA duplex consists of 18 bp with a 5′ overhang on each strand.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkr1250-F3: The C.Esp1396I OL nucleoprotein complex structure. The asymmetric unit of the crystal contains a C.Esp1396I dimer (chains A and B; blue and green, respectively) bound to DNA (chains C and D; beige and pink, respectively). The DNA duplex consists of 18 bp with a 5′ overhang on each strand.
Mentions: One complex, consisting of a C.Esp1396I dimer bound to a DNA duplex (Figure 3), is present in the asymmetric unit and the structure refined to 2.1 Å with a final R/Rfree of 16.8/22.4% (Table 1). Iterative refinement was carried out using Refmac (19) with TLS restraints enabled. All of the DNA bases are clearly resolved, as are all except a few amino acid residues at the N and C termini of each protein subunit. In addition, a total of 314 solvent molecules could be located, including a number of water molecules mediating protein–DNA interactions.Figure 3.

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