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Checkpoints throughout the cell cycle serve as safeguards and gatekeepers, allowing the cell cycle to progress in favorable conditions and slow or halt it in problematic ones. This regulation is known as the cell cycle control system.
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Structural and Functional Analysis of the Cdk13/Cyclin K Complex.

Ann Katrin Greifenberg1, Dana Hönig2, Kveta Pilarova3

  • 1Institute of Innate Immunity, Department of Structural Immunology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany; Center of Advanced European Studies and Research, Group Physical Biochemistry, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.

Cell Reports
|January 11, 2016
PubMed
Summary

Researchers elucidated the structure and function of human Cyclin-dependent kinase 13 (Cdk13)/Cyclin K. This complex phosphorylates RNA polymerase II C-terminal domain, impacting gene expression and growth signaling pathways.

Keywords:
Cdk13Cyclin KPin1RNA polymerase IIflavopiridolIntroductiontranscription

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Cyclin-dependent kinases (CDKs) are crucial regulators of eukaryotic cell cycle and transcription.
  • Understanding the specific roles and mechanisms of CDKs like Cdk13 is essential for deciphering gene regulation.

Purpose of the Study:

  • To determine the crystal structure of the human Cdk13/Cyclin K complex.
  • To investigate the substrate specificity and regulatory interactions of Cdk13.
  • To explore the functional consequences of Cdk13 activity on gene expression.

Main Methods:

  • X-ray crystallography to determine the 2.0 Å resolution structure of Cdk13/Cyclin K.
  • In vitro kinase assays using recombinant proteins to assess phosphorylation.
  • RNA polymerase II C-terminal domain (CTD) phosphorylation site analysis.
  • Analysis of gene expression changes following Cdk13 or Cdk12 knockdown.
  • Enzyme inhibition assays with flavopiridol.

Main Results:

  • The crystal structure of Cdk13/Cyclin K revealed a C-terminal extension helix with a polybasic cluster and DCHEL motif interacting with ATP.
  • Cdk13/CycK phosphorylates Ser5 and Ser2 of the RNA polymerase II CTD, preferring Ser7 pre-phosphorylations.
  • The peptidyl-prolyl isomerase Pin1 interacts with the phosphorylated CTD but does not alter kinase specificity.
  • Flavopiridol inhibits Cdk7 more potently than Cdk13.
  • Knockdown of Cdk13 or Cdk12 resulted in distinct gene expression profiles, with Cdk13-dependent genes enriched in growth signaling pathways.

Conclusions:

  • The study provides structural and functional insights into human Cdk13/CycK.
  • Cdk13 plays a significant role in regulating transcription, particularly impacting growth signaling pathways.
  • Cdk13's phosphorylation activity on the RNA polymerase II CTD is a key mechanism in its regulatory function.