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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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Triple helical DNA interactions between symmetry related 19-mer complexes. (a) The triple helical interactions occur between A1 and G19 of chain C (blue and beige, respectively) and T′1 and A′19 of chain D (pink and green, respectively). (b) A cartoon representation depicting how the Watson–crick edge of the overhanging 5′ base (either T′1 or A1) forms hydrogen bonds with the Hoogstein edge of the terminal base of a symmetry related molecule (A′19 or G19, respectively).
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gkr1250-F2: Triple helical DNA interactions between symmetry related 19-mer complexes. (a) The triple helical interactions occur between A1 and G19 of chain C (blue and beige, respectively) and T′1 and A′19 of chain D (pink and green, respectively). (b) A cartoon representation depicting how the Watson–crick edge of the overhanging 5′ base (either T′1 or A1) forms hydrogen bonds with the Hoogstein edge of the terminal base of a symmetry related molecule (A′19 or G19, respectively).

Mentions: The DNA sequence (an 18-bp duplex with an overhanging base at the 5′-end of each strand) was designed to aid the formation of pseudo-continuous DNA in a single orientation and thus overcome the symmetry-averaging problems encountered in the tetramer complex structure (11). The averaging problem was indeed overcome in this structure, but the DNA did not form a pseudo-continuous helix. Instead, the DNA ends are involved in crystal packing interactions between symmetry related molecules and form triple helical interactions (Figure 2). The terminal two bases are paired on both the Hoogstein and Watson–Crick edges to form a base ‘triplet’ at both ends of the DNA (T-AT and A-GC), which maximizes base stacking. These triple helical interactions help to stabilize the DNA ends, which refined with low B-factors, despite not being involved in protein–DNA interactions.Figure 2.


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)

Triple helical DNA interactions between symmetry related 19-mer complexes. (a) The triple helical interactions occur between A1 and G19 of chain C (blue and beige, respectively) and T′1 and A′19 of chain D (pink and green, respectively). (b) A cartoon representation depicting how the Watson–crick edge of the overhanging 5′ base (either T′1 or A1) forms hydrogen bonds with the Hoogstein edge of the terminal base of a symmetry related molecule (A′19 or G19, respectively).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkr1250-F2: Triple helical DNA interactions between symmetry related 19-mer complexes. (a) The triple helical interactions occur between A1 and G19 of chain C (blue and beige, respectively) and T′1 and A′19 of chain D (pink and green, respectively). (b) A cartoon representation depicting how the Watson–crick edge of the overhanging 5′ base (either T′1 or A1) forms hydrogen bonds with the Hoogstein edge of the terminal base of a symmetry related molecule (A′19 or G19, respectively).
Mentions: The DNA sequence (an 18-bp duplex with an overhanging base at the 5′-end of each strand) was designed to aid the formation of pseudo-continuous DNA in a single orientation and thus overcome the symmetry-averaging problems encountered in the tetramer complex structure (11). The averaging problem was indeed overcome in this structure, but the DNA did not form a pseudo-continuous helix. Instead, the DNA ends are involved in crystal packing interactions between symmetry related molecules and form triple helical interactions (Figure 2). The terminal two bases are paired on both the Hoogstein and Watson–Crick edges to form a base ‘triplet’ at both ends of the DNA (T-AT and A-GC), which maximizes base stacking. These triple helical interactions help to stabilize the DNA ends, which refined with low B-factors, despite not being involved in protein–DNA interactions.Figure 2.

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