Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35147.16 
• Atom Count: 2491 
• Residue Count: 302 
• Unique protein chains: 1

2W4K

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

• DOI: 10.2210/pdb2W4K/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2008-11-27 Released: 2009-12-22 
• Deposition Author(s): De Diego, I., Kuper, J., Lehmann, F., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 

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

• PubMed: 24440081 
• DOI: 10.1016/j.chembiol.2013.12.008
• Primary Citation of Related Structures:  
  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 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.

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Organizational Affiliation: 

European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22603 Hamburg, Germany; European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DEATH-ASSOCIATED PROTEIN KINASE 1	A	302	Homo sapiens	Mutation(s): 0  Gene Names: DAPK1 (DAPK) EC: 2.7.11.1
Find proteins for P53355 (Homo sapiens) Go to Gene View: DAPK1 Go to UniProtKB:  P53355

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 49.310	α = 90.00
b = 76.970	β = 90.00
c = 108.936	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-27 
• Released Date: 2009-12-22 
• Deposition Author(s): De Diego, I., Kuper, J., Lehmann, F., Wilmanns, M.

Revision History 

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