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 1YRP | pdb_00001yrp

Catalytic domain of human ZIP kinase phosphorylated at Thr265


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.268 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1YRP

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 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.

Macromolecule Content 

  • Total Structure Weight: 64.27 kDa 
  • Atom Count: 4,498 
  • Modeled Residue Count: 552 
  • Deposited Residue Count: 556 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Death-associated protein kinase 3
A, B
278Homo sapiensMutation(s): 0 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O43293 (Homo sapiens)
Explore O43293 
Go to UniProtKB:  O43293
PHAROS:  O43293
GTEx:  ENSG00000167657 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43293
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTT

Query on DTT



Download:Ideal Coordinates CCD File
C [auth B]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.268 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.56α = 90
b = 60.93β = 92.17
c = 87.95γ = 90
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: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2016-05-18
    Changes: Database references
  • Version 1.4: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary