1YRP

Catalytic domain of human ZIP kinase phosphorylated at Thr265


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.str.2016.03.020
  • Primary Citation of Related Structures:  

  • 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-depend ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death-associated protein kinase 3
A, B
278Homo sapiensMutation(s): 0 
Gene Names: DAPK3 (ZIPK)
EC: 2.7.11.1
Find proteins for O43293 (Homo sapiens)
Go to Gene View: DAPK3
Go to UniProtKB:  O43293
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT

Download SDF File 
Download CCD File 
B
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.560α = 90.00
b = 60.930β = 92.17
c = 87.950γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2016-05-18
    Type: Database references