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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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Direct and indirect readout of DNA by R35. (a) The R35 recognizes the G3 and G17 in the DNA sequence and the highlighted bases (beige: chain C and pink: chain D) are shown in b and c. (b) The R35 from chain A recognizes the conserved TG by interacting with the O6 and N7 of the guanine base. The planar guanidinium group of R35 also stacks with the thymine base. (c) The symmetry related interaction cannot be made by chain B, which instead recognizes G17 via the O6 and N7. All hydrogen bond distances are <3.2 Å.
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gkr1250-F4: Direct and indirect readout of DNA by R35. (a) The R35 recognizes the G3 and G17 in the DNA sequence and the highlighted bases (beige: chain C and pink: chain D) are shown in b and c. (b) The R35 from chain A recognizes the conserved TG by interacting with the O6 and N7 of the guanine base. The planar guanidinium group of R35 also stacks with the thymine base. (c) The symmetry related interaction cannot be made by chain B, which instead recognizes G17 via the O6 and N7. All hydrogen bond distances are <3.2 Å.

Mentions: The amino groups of R35 in each subunit interact with the N7 and O6 of a guanine. R35 in chain A recognizes G3 on one DNA strand (Figure 4a,b). However, the R35 in chain B cannot make the symmetry equivalent interaction on the other strand, as an adenine (A′3) rather than a guanine is in the equivalent position in chain D. Instead, the R35 interacts with the N7 and O6 of the G17 on chain C (Figure 4c); it is clear that the flexible side-chain of arginine is capable of accommodating the departure from dyad symmetry in the OL DNA sequence. In addition to hydrogen bonding with G3, R35 in chain A is involved in indirect readout by stacking of the planar guanidinium group with the exposed face of T2 as described elsewhere (11) and is thus specific for a TG dinucleotide at this position. There is no equivalent stacking of R35 of chain B, however, since there is no equivalent TG dinucleotide at this site (there is an adjacent T but it is on the 3′ side of the G, which therefore adopts a very different base stacking pattern).Figure 4.


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)

Direct and indirect readout of DNA by R35. (a) The R35 recognizes the G3 and G17 in the DNA sequence and the highlighted bases (beige: chain C and pink: chain D) are shown in b and c. (b) The R35 from chain A recognizes the conserved TG by interacting with the O6 and N7 of the guanine base. The planar guanidinium group of R35 also stacks with the thymine base. (c) The symmetry related interaction cannot be made by chain B, which instead recognizes G17 via the O6 and N7. All hydrogen bond distances are <3.2 Å.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkr1250-F4: Direct and indirect readout of DNA by R35. (a) The R35 recognizes the G3 and G17 in the DNA sequence and the highlighted bases (beige: chain C and pink: chain D) are shown in b and c. (b) The R35 from chain A recognizes the conserved TG by interacting with the O6 and N7 of the guanine base. The planar guanidinium group of R35 also stacks with the thymine base. (c) The symmetry related interaction cannot be made by chain B, which instead recognizes G17 via the O6 and N7. All hydrogen bond distances are <3.2 Å.
Mentions: The amino groups of R35 in each subunit interact with the N7 and O6 of a guanine. R35 in chain A recognizes G3 on one DNA strand (Figure 4a,b). However, the R35 in chain B cannot make the symmetry equivalent interaction on the other strand, as an adenine (A′3) rather than a guanine is in the equivalent position in chain D. Instead, the R35 interacts with the N7 and O6 of the G17 on chain C (Figure 4c); it is clear that the flexible side-chain of arginine is capable of accommodating the departure from dyad symmetry in the OL DNA sequence. In addition to hydrogen bonding with G3, R35 in chain A is involved in indirect readout by stacking of the planar guanidinium group with the exposed face of T2 as described elsewhere (11) and is thus specific for a TG dinucleotide at this position. There is no equivalent stacking of R35 of chain B, however, since there is no equivalent TG dinucleotide at this site (there is an adjacent T but it is on the 3′ side of the G, which therefore adopts a very different base stacking pattern).Figure 4.

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