2W4K

X-ray structure of a DAP-Kinase 2-302

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A Pef/Y Substrate Recognition and Signature Motif Plays a Critical Role in Dapk-Related Kinase Activity.

Temmerman, K., De Diego, I., Pogenberg, V., Simon, B., Jonko, W., Li, X., Wilmanns, M.

(2014) Chem Biol 21: 264

  • DOI: 10.1016/j.chembiol.2013.12.008
  • Primary Citation of Related Structures:  
    2W4K, 4B4L, 2XUU

  • PubMed Abstract: 

    • Knowledge about protein kinase substrate preferences is biased toward residues immediately adjacent to the site of phosphorylation. By a combined structural, biochemical, and cellular approach, we have discovered an unexpected substrate recognition e ...

    Knowledge about protein kinase substrate preferences is biased toward residues immediately adjacent to the site of phosphorylation. By a combined structural, biochemical, and cellular approach, we have discovered an unexpected substrate recognition element with the consensus sequence PEF/Y in the tumor suppressor death-associated protein kinase 1. This motif can be effectively blocked by a specific pseudosubstrate-type interaction with an autoregulatory domain of this kinase. In this arrangement, the central PEF/Y glutamate interacts with a conserved arginine distant to the phosphorylation site in sequence and structure. We also demonstrate that the element is crucial for kinase activity regulation and substrate recognition. The PEF/Y motif distinguishes close death-associated protein kinase relatives from canonical calcium/calmodulin-dependent protein kinases. Insight into this signature and mode of action offers new opportunities to identify specific small molecule inhibitors in PEF/Y-containing protein kinases.

    Organizational Affiliation: 

    European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22603 Hamburg, Germany. Electronic address: wilmanns@embl-hamburg.de.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEATH-ASSOCIATED PROTEIN KINASE 1A302Homo sapiensMutation(s): 0 
Gene Names: DAPK1, DAPK
EC: 2.7.11.1
Find proteins for P53355 (Homo sapiens)
Explore P53355 
Go to UniProtKB:  P53355
NIH Common Fund Data Resources
PHAROS  P53355
GTEx  ENSG00000196730
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.31α = 90
b = 76.97β = 90
c = 108.936γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2014-03-05
    Changes: Database references