4NST

Crystal structure of human Cdk12/Cyclin K in complex with ADP-aluminum fluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure and substrate specificity of human Cdk12/Cyclin K.

Bosken, C.A.Farnung, L.Hintermair, C.Merzel Schachter, M.Vogel-Bachmayr, K.Blazek, D.Anand, K.Fisher, R.P.Eick, D.Geyer, M.

(2014) Nat Commun 5: 3505-3505

  • DOI: 10.1038/ncomms4505

  • PubMed Abstract: 
  • Phosphorylation of the RNA polymerase II C-terminal domain (CTD) by cyclin-dependent kinases is important for productive transcription. Here we determine the crystal structure of Cdk12/CycK and analyse its requirements for substrate recognition. Acti ...

    Phosphorylation of the RNA polymerase II C-terminal domain (CTD) by cyclin-dependent kinases is important for productive transcription. Here we determine the crystal structure of Cdk12/CycK and analyse its requirements for substrate recognition. Active Cdk12/CycK is arranged in an open conformation similar to that of Cdk9/CycT but different from those of cell cycle kinases. Cdk12 contains a C-terminal extension that folds onto the N- and C-terminal lobes thereby contacting the ATP ribose. The interaction is mediated by an HE motif followed by a polybasic cluster that is conserved in transcriptional CDKs. Cdk12/CycK showed the highest activity on a CTD substrate prephosphorylated at position Ser7, whereas the common Lys7 substitution was not recognized. Flavopiridol is most potent towards Cdk12 but was still 10-fold more potent towards Cdk9. T-loop phosphorylation of Cdk12 required coexpression with a Cdk-activating kinase. These results suggest the regulation of Pol II elongation by a relay of transcriptionally active CTD kinases.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany.,Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic.,Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany.,1] Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany [2] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany.,Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science (CIPSM), Marchioninistrasse 25, M√ľnchen 81377, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 12
A, C
351Homo sapiensMutation(s): 0 
Gene Names: CDK12 (CRK7, CRKRS, KIAA0904)
EC: 2.7.11.22, 2.7.11.23
Find proteins for Q9NYV4 (Homo sapiens)
Go to Gene View: CDK12
Go to UniProtKB:  Q9NYV4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-K
B, D
268Homo sapiensMutation(s): 0 
Gene Names: CCNK (CPR4)
Find proteins for O75909 (Homo sapiens)
Go to Gene View: CCNK
Go to UniProtKB:  O75909
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AF3
Query on AF3

Download SDF File 
Download CCD File 
A, C
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.720α = 104.04
b = 78.850β = 85.76
c = 91.490γ = 101.46
Software Package:
Software NamePurpose
XSCALEdata scaling
ADSCdata collection
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references