1Z57

Crystal structure of human CLK1 in complex with 10Z-Hymenialdisine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Kinase domain insertions define distinct roles of CLK kinases in SR protein phosphorylation.

Bullock, A.N.Das, S.Debreczeni, J.E.Rellos, P.Fedorov, O.Niesen, F.H.Guo, K.Papagrigoriou, E.Amos, A.L.Cho, S.Turk, B.E.Ghosh, G.Knapp, S.

(2009) Structure 17: 352-362

  • DOI: 10.1016/j.str.2008.12.023
  • Primary Citation of Related Structures:  
    1Z57, 2EU9

  • PubMed Abstract: 
  • Splicing requires reversible phosphorylation of serine/arginine-rich (SR) proteins, which direct splice site selection in eukaryotic mRNA. These phosphorylation events are dependent on SR protein (SRPK) and cdc2-like kinase (CLK) families. SRPK1 phos ...

    Splicing requires reversible phosphorylation of serine/arginine-rich (SR) proteins, which direct splice site selection in eukaryotic mRNA. These phosphorylation events are dependent on SR protein (SRPK) and cdc2-like kinase (CLK) families. SRPK1 phosphorylation of splicing factors is restricted by a specific docking interaction whereas CLK activity is less constrained. To understand functional differences between splicing factor targeting kinases, we determined crystal structures of CLK1 and CLK3. Intriguingly, in CLKs the SRPK1 docking site is blocked by insertion of a previously unseen helix alphaH. In addition, substrate docking grooves present in related mitogen activating protein kinases (MAPKs) are inaccessible due to a CLK specific beta7/8-hairpin insert. Thus, the unconstrained substrate interaction together with the determined active-site mediated substrate specificity allows CLKs to complete the functionally important hyperphosphorylation of splicing factors like ASF/SF2. In addition, despite high sequence conservation, we identified inhibitors with surprising isoform specificity for CLK1 over CLK3.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Old Road Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK. alex.bullock@sgc.ox.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK1A339Homo sapiensMutation(s): 0 
Gene Names: CLK1CLK
EC: 2.7.12.1
Find proteins for P49759 (Homo sapiens)
Explore P49759 
Go to UniProtKB:  P49759
NIH Common Fund Data Resources
PHAROS  P49759
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DBQ
Query on DBQ

Download CCD File 
A
DEBROMOHYMENIALDISINE
C11 H11 N5 O2
JYRJOQGKGMHTOO-VURMDHGXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.277α = 90
b = 64.434β = 119.19
c = 80.112γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-05-09
    Changes: Other
  • Version 1.4: 2012-08-29
    Changes: Database references