2A2A

High-resolution crystallographic analysis of the autoinhibited conformation of a human death-associated protein kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites

Simon, B.Huart, A.S.Temmerman, K.Vahokoski, J.Mertens, H.D.Komadina, D.Hoffmann, J.E.Yumerefendi, H.Svergun, D.I.Kursula, P.Schultz, C.McCarthy, A.A.Hart, D.J.Wilmanns, M.

(2016) Structure 

  • DOI: https://doi.org/10.1016/j.str.2016.03.020
  • Primary Citation of Related Structures:  
    1YRP, 2A2A, 2XZS

  • PubMed Abstract: 

    The regulation of many protein kinases by binding to calcium/calmodulin connects two principal mechanisms in signaling processes: protein phosphorylation and responses to dose- and time-dependent calcium signals. We used the calcium/calmodulin-dependent members of the death-associated protein kinase (DAPK) family to investigate the role of a basic DAPK signature loop near the kinase active site. In DAPK2, this loop comprises a novel dimerization-regulated calcium/calmodulin-binding site, in addition to a well-established calcium/calmodulin site in the C-terminal autoregulatory domain. Unexpectedly, impairment of the basic loop interaction site completely abolishes calcium/calmodulin binding and DAPK2 activity is reduced to a residual level, indicative of coupled binding to the two sites. This contrasts with the generally accepted view that kinase calcium/calmodulin interactions are autonomous of the kinase catalytic domain. Our data establish an intricate model of multi-step kinase activation and expand our understanding of how calcium binding connects with other mechanisms involved in kinase activity regulation.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Death-associated protein kinase 2
A, B, C, D
321Homo sapiensMutation(s): 0 
EC: 2.7.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIK4 (Homo sapiens)
Explore Q9UIK4 
Go to UniProtKB:  Q9UIK4
PHAROS:  Q9UIK4
GTEx:  ENSG00000035664 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIK4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
R [auth C],
U [auth D]
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
S [auth C],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
Q [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
N [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
T [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.3α = 92.16
b = 60.65β = 103.45
c = 98.71γ = 94.25
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2016-05-18
    Changes: Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description