3OHT

Crystal Structure of Salmo Salar p38alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

p38alpha MAP kinase dimers with swapped activation segments and a novel catalytic loop conformation

Rothweiler, U.Aberg, E.Johnson, K.A.Hansen, T.E.Jorgensen, J.B.Engh, R.A.

(2011) J Mol Biol 411: 474-485

  • DOI: https://doi.org/10.1016/j.jmb.2011.06.013
  • Primary Citation of Related Structures:  
    3OHT

  • PubMed Abstract: 

    Many protein kinase functions, including autophosphorylation in trans, require dimerization, possibly by activation segment exchange. Such dimers have been reported for a few autophosphorylating protein kinases, but not for mitogen-activated protein kinases (MAPKs). Activation of MAPKs proceeds not only via the well-characterized action of dual T/Y specificity MAPK kinases, phosphorylating both residues of the MAPK TxY activation loop motif, but also via a noncanonical activation pathway triggered by phosphorylation at Tyr323 and homodimerization. Here, we report the 2. 7-Å-resolution structure of p38α MAPK from Salmo salar in a novel domain-swapped homodimeric form. The tyrosines of the conserved sequence YxAPE anchor the swapped activation segments in a configuration suitable for autophosphorylation in trans and provide a model for the noncanonical pathway. In the dimer, a structural unit containing Tyr323 is formed at a dimerization contact region that stabilizes the HRD catalytic loop in a unique inactive geometry. This feature is consistent with the requirement of Tyr323 phosphorylation for the initiation of the noncanonical pathway. Despite the interacting surface of more than 2600 Å(2), the dimer is not obligate, as gel filtration shows the dimerization to occur only at relatively high concentrations. The transition from monomer to dimer involves a relatively simple hinged displacement of helix EF and adjacent residues. Thus, dimer formation is likely to be transient, compatible with functional requirements for autophosphorylation, allowing further modulation, for example, by scaffolding mechanisms.


  • Organizational Affiliation

    Department of Chemistry, The Norwegian Structural Biology Centre, University of Tromsø, 9037 Tromsø, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
p38a
A, B
389Salmo salarMutation(s): 0 
Gene Names: p38a
UniProt
Find proteins for A9UJZ9 (Salmo salar)
Explore A9UJZ9 
Go to UniProtKB:  A9UJZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9UJZ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
1N1 BindingDB:  3OHT Kd: min: 27, max: 495 (nM) from 3 assay(s)
EC50: 470 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.78α = 90
b = 100.93β = 98.15
c = 67.89γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-27
    Changes: Database references, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description