Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 41.23 kDa 
• Atom Count: 2900 
• Modelled Residue Count: 332 
• Deposited Residue Count: 360 
• Unique protein chains: 1

4E5A

The W197A mutant of p38a MAP kinase

• PDB DOI: 10.2210/pdb4E5A/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-03-14 Released: 2012-10-31 
• Deposition Author(s): Livnah, O., Tzarum, N., Eisenberg-Domovich, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.253 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Lipid Molecules Induce p38 alpha Activation via a Novel Molecular Switch.

Tzarum, N., Eisenberg-Domovich, Y., Gills, J.J., Dennis, P.A., Livnah, O.

(2012) J Mol Biol 424: 339-353

• PubMed: 23079240 
• DOI: 10.1016/j.jmb.2012.10.007
• Primary Citation of Related Structures:  
  4E5A, 4E5B, 4E6A, 4E6C, 4E8A


• PubMed Abstract: 
  

p38α mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analogues (PIA) inducing p38α autoactivation and apoptosis. Perifosine, an Akt inhibitor in phase II clinical trials, also showed p38α activation properties similarly to those of PIAs. The crystal structures of p38α in complex with PIA23, PIA24 and perifosine provide insights into this unique activation mode. The activating molecules bind a unique hydrophobic binding site in the kinase C'-lobe formed in part by the MAPK insert region. In addition, there are conformational changes in the short αEF/αF loop region that acts as an activation switch, inducing autophosphorylation. Structural and biochemical characterization of the αEF/αF loop identified Trp197 as a key residue in the lipid binding and in p38α catalytic activity. The lipid binding site also accommodates hydrophobic inhibitor molecules and, thus, can serve as a novel p38α-target for specific activation or inhibition, with novel therapeutic implications.

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Organizational Affiliation: 

Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences and The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A [auth X]	360	Homo sapiens	Mutation(s): 1  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.253 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.493	α = 90
b = 75.74	β = 90
c = 76.588	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-14 
• Released Date: 2012-10-31 
Deposition Author(s): Livnah, O., Tzarum, N., Eisenberg-Domovich, Y.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary