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Binding to DNA of the RNA-polymerase II C-terminal domain allows discrimination between Cdk7 and Cdk9 phosphorylation.

Lolli G - Nucleic Acids Res. (2009)

Bottom Line: Model-building studies indicate the structural mechanism underlying such specificity involves interaction of Cdk7 with DNA in the context of the CTD/DNA complex.CTD dissociates from DNA following phosphorylation by Cdk7, allowing transcription initiation.The CTD then becomes accessible for further phosphorylation by Cdk9 that drives the transition to transcription elongation.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. graziano@biop.ox.ac.uk

ABSTRACT
The C-terminal domain (CTD) of RNA polymerase II regulates transcription through spatially and temporally coordinated events. Previous work had established that the CTD binds DNA but the significance of this interaction has not been determined. The present work shows that the CTD binds DNA in its unphosphorylated form, the form in which it is present in the pre-initiation complex. The CTD/DNA complex is recognized by and is phosphorylated by Cdk7 but not by Cdk9. Model-building studies indicate the structural mechanism underlying such specificity involves interaction of Cdk7 with DNA in the context of the CTD/DNA complex. The model has been tested by mutagenesis experiments. CTD dissociates from DNA following phosphorylation by Cdk7, allowing transcription initiation. The CTD then becomes accessible for further phosphorylation by Cdk9 that drives the transition to transcription elongation.

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Related in: MedlinePlus

CTD/DNA complex and model of interaction with Cdk7/CycH. (A) Two different views of the CTD/DNA complex (left) and their surface representation (right). DNA is in yellow, CTD in magenta, Ser5 in blue and Ser2 in grey. Ser5 is exposed while Ser2 is poorly accessible. (B) CTD/DNA docked inside Cdk7/CycH active site. DNA is in yellow, CTD in magenta, Cdk7 in green and CycH in cyan. Polar interactions are represented as dotted lines. CTD Ser5 is in contact with Cdk7 catalytic Asp137 and Lys139. A basic stretch of amino acids in Cdk7 contacts DNA backbone.
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Figure 2: CTD/DNA complex and model of interaction with Cdk7/CycH. (A) Two different views of the CTD/DNA complex (left) and their surface representation (right). DNA is in yellow, CTD in magenta, Ser5 in blue and Ser2 in grey. Ser5 is exposed while Ser2 is poorly accessible. (B) CTD/DNA docked inside Cdk7/CycH active site. DNA is in yellow, CTD in magenta, Cdk7 in green and CycH in cyan. Polar interactions are represented as dotted lines. CTD Ser5 is in contact with Cdk7 catalytic Asp137 and Lys139. A basic stretch of amino acids in Cdk7 contacts DNA backbone.

Mentions: To understand these different recognition properties, a model of the CTD/DNA complex was built based on the NMR model of a dsDNA hexamer in complex with the YSPTSPSY CTD peptide (21) and on the crystal structures of DNA–triostin A complex (PDB 185D and 1VS2) (29–31). Triostin A is a bis-intercalating antibiotic mimicking the binding mode to DNA of single CTD repeats (24). In the model of the DNA/CTD complex, Ser5 is exposed but Ser2 is buried because of its proximity to the buried tyrosine of the CTD (Figure 2A). The CTD is in a beta-turn conformation generated by the DNA-intercalating tyrosines (21).Figure 2.


Binding to DNA of the RNA-polymerase II C-terminal domain allows discrimination between Cdk7 and Cdk9 phosphorylation.

Lolli G - Nucleic Acids Res. (2009)

CTD/DNA complex and model of interaction with Cdk7/CycH. (A) Two different views of the CTD/DNA complex (left) and their surface representation (right). DNA is in yellow, CTD in magenta, Ser5 in blue and Ser2 in grey. Ser5 is exposed while Ser2 is poorly accessible. (B) CTD/DNA docked inside Cdk7/CycH active site. DNA is in yellow, CTD in magenta, Cdk7 in green and CycH in cyan. Polar interactions are represented as dotted lines. CTD Ser5 is in contact with Cdk7 catalytic Asp137 and Lys139. A basic stretch of amino acids in Cdk7 contacts DNA backbone.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651791&req=5

Figure 2: CTD/DNA complex and model of interaction with Cdk7/CycH. (A) Two different views of the CTD/DNA complex (left) and their surface representation (right). DNA is in yellow, CTD in magenta, Ser5 in blue and Ser2 in grey. Ser5 is exposed while Ser2 is poorly accessible. (B) CTD/DNA docked inside Cdk7/CycH active site. DNA is in yellow, CTD in magenta, Cdk7 in green and CycH in cyan. Polar interactions are represented as dotted lines. CTD Ser5 is in contact with Cdk7 catalytic Asp137 and Lys139. A basic stretch of amino acids in Cdk7 contacts DNA backbone.
Mentions: To understand these different recognition properties, a model of the CTD/DNA complex was built based on the NMR model of a dsDNA hexamer in complex with the YSPTSPSY CTD peptide (21) and on the crystal structures of DNA–triostin A complex (PDB 185D and 1VS2) (29–31). Triostin A is a bis-intercalating antibiotic mimicking the binding mode to DNA of single CTD repeats (24). In the model of the DNA/CTD complex, Ser5 is exposed but Ser2 is buried because of its proximity to the buried tyrosine of the CTD (Figure 2A). The CTD is in a beta-turn conformation generated by the DNA-intercalating tyrosines (21).Figure 2.

Bottom Line: Model-building studies indicate the structural mechanism underlying such specificity involves interaction of Cdk7 with DNA in the context of the CTD/DNA complex.CTD dissociates from DNA following phosphorylation by Cdk7, allowing transcription initiation.The CTD then becomes accessible for further phosphorylation by Cdk9 that drives the transition to transcription elongation.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. graziano@biop.ox.ac.uk

ABSTRACT
The C-terminal domain (CTD) of RNA polymerase II regulates transcription through spatially and temporally coordinated events. Previous work had established that the CTD binds DNA but the significance of this interaction has not been determined. The present work shows that the CTD binds DNA in its unphosphorylated form, the form in which it is present in the pre-initiation complex. The CTD/DNA complex is recognized by and is phosphorylated by Cdk7 but not by Cdk9. Model-building studies indicate the structural mechanism underlying such specificity involves interaction of Cdk7 with DNA in the context of the CTD/DNA complex. The model has been tested by mutagenesis experiments. CTD dissociates from DNA following phosphorylation by Cdk7, allowing transcription initiation. The CTD then becomes accessible for further phosphorylation by Cdk9 that drives the transition to transcription elongation.

Show MeSH
Related in: MedlinePlus