4CXA

Crystal structure of the human CDK12-cyclin K complex bound to AMPPNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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Literature

Structures of the Cdk12/Cyck Complex with AMP-Pnp Reveal a Flexible C-Terminal Kinase Extension Important for ATP Binding.

Dixon-Clarke, S.E., Elkins, J.M., Cheng, S.G., Morin, G.B., Bullock, A.N.

(2015) Sci Rep 5: 17122

  • DOI: 10.1038/srep17122
  • Primary Citation of Related Structures:  
    4CXA, 4UN0

  • PubMed Abstract: 

    • Cyclin-dependent kinase 12 (CDK12) promotes transcriptional elongation by phosphorylation of the RNA polymerase II C-terminal domain (CTD). Structure-function studies show that this activity is dependent on a C-terminal kinase extension, as well as the binding of cyclin K (CycK) ...

    Cyclin-dependent kinase 12 (CDK12) promotes transcriptional elongation by phosphorylation of the RNA polymerase II C-terminal domain (CTD). Structure-function studies show that this activity is dependent on a C-terminal kinase extension, as well as the binding of cyclin K (CycK). To better define these interactions we determined the crystal structure of the human CDK12/CycK complex with and without the kinase extension in the presence of AMP-PNP. The structures revealed novel features for a CDK, including a large β4-β5 loop insertion that contributes to the N-lobe interaction with the cyclin. We also observed two different conformations of the C-terminal kinase extension that effectively open and close the ATP pocket. Most notably, bound AMP-PNP was only observed when trapped in the closed state. Truncation of this C-terminal structure also diminished AMP-PNP binding, as well as the catalytic activity of the CDK12/CycK complex. Further kinetic measurements showed that the full length CDK12/CycK complex was significantly more active than the two crystallised constructs suggesting a critical role for additional domains. Overall, these results demonstrate the intrinsic flexibility of the C-terminal extension in CDK12 and highlight its importance for both ATP binding and kinase activity.

    Organizational Affiliation: 

    Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 12A, C340Homo sapiensMutation(s): 0 
Gene Names: CDK12, CRK7, CRKRS, KIAA0904
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYV4 (Homo sapiens)
Explore Q9NYV4 
Go to UniProtKB:  Q9NYV4
PHAROS:  Q9NYV4
GTEx:  ENSG00000167258 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYV4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-KB, D259Homo sapiensMutation(s): 0 
Gene Names: CCNK, CPR4
UniProt & NIH Common Fund Data Resources
Find proteins for O75909 (Homo sapiens)
Explore O75909 
Go to UniProtKB:  O75909
PHAROS:  O75909
GTEx:  ENSG00000090061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75909
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
E [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 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: 3.15 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.843α = 90
b = 138.791β = 104.99
c = 71.888γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references