Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 83.94 kDa 
• Atom Count: 5357 
• Modelled Residue Count: 598 
• Deposited Residue Count: 722 
• Unique protein chains: 1

2YA9

Crystal structure of the autoinhibited form of mouse DAPK2

• PDB DOI: 10.2210/pdb2YA9/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-18 Released: 2011-04-13 
• Deposition Author(s): Patel, A.K., Kursula, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Structure of the Dimeric Autoinhibited Conformation of Dapk2, a Pro-Apoptotic Protein Kinase.

Patel, A.K., Yadav, R.P., Majava, V., Kursula, I., Kursula, P.

(2011) J Mol Biol 409: 369

• PubMed: 21497605 
• DOI: 10.1016/j.jmb.2011.03.065
• Primary Citation of Related Structures:  
  2YA9, 2YAA, 2YAB


• PubMed Abstract: 
  

The death-associated protein kinase (DAPK) family has been characterized as a group of pro-apoptotic serine/threonine kinases that share specific structural features in their catalytic kinase domain. Two of the DAPK family members, DAPK1 and DAPK2, are calmodulin-dependent protein kinases that are regulated by oligomerization, calmodulin binding, and autophosphorylation. In this study, we have determined the crystal and solution structures of murine DAPK2 in the presence of the autoinhibitory domain, with and without bound nucleotides in the active site. The crystal structure shows dimers of DAPK2 in a conformation that is not permissible for protein substrate binding. Two different conformations were seen in the active site upon the introduction of nucleotide ligands. The monomeric and dimeric forms of DAPK2 were further analyzed for solution structure, and the results indicate that the dimers of DAPK2 are indeed formed through the association of two apposed catalytic domains, as seen in the crystal structure. The structures can be further used to build a model for DAPK2 autophosphorylation and to compare with closely related kinases, of which especially DAPK1 is an actively studied drug target. Our structures also provide a model for both homodimerization and heterodimerization of the catalytic domain between members of the DAPK family. The fingerprint of the DAPK family, the basic loop, plays a central role in the dimerization of the kinase domain.

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Organizational Affiliation: 

Department of Biochemistry, University of Oulu, Finland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEATH-ASSOCIATED PROTEIN KINASE 2	A, B	361	Mus musculus	Mutation(s): 0  Gene Names: Dapk2 EC: 2.7.11.1
UniProt
Find proteins for Q8VDF3 (Mus musculus) Explore Q8VDF3  Go to UniProtKB:  Q8VDF3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D1D	C [auth A], E [auth B]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-QWWZWVQMSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.04	α = 90
b = 86.44	β = 90
c = 124.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-18 
• Released Date: 2011-04-13 
Deposition Author(s): Patel, A.K., Kursula, P.

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references, Version format compliance