Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.61 kDa 
• Atom Count: 4807 
• Residue Count: 661 
• Unique protein chains: 1

4IC8

Crystal structure of the apo ERK5 kinase domain

• DOI: 10.2210/pdb4IC8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-10 Released: 2013-02-13 
• Deposition Author(s): Gogl, G., Remenyi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.290 
• R-Value Work: 0.262 
• R-Value Observed: 0.263 

Literature

Structural mechanism for the specific assembly and activation of the extracellular signal regulated kinase 5 (ERK5) module.

Glatz, G., Gogl, G., Alexa, A., Remenyi, A.

(2013) J Biol Chem 288: 8596-8609

• PubMed: 23382384 
• DOI: 10.1074/jbc.M113.452235
• Primary Citation of Related Structures:  
  4IC7, 4IC8


• PubMed Abstract: 
  

Mitogen-activated protein kinase (MAPK) activation depends on a linear binding motif found in all MAPK kinases (MKK). In addition, the PB1 (Phox and Bem1) domain of MKK5 is required for extracellular signal regulated kinase 5 (ERK5) activation. We present the crystal structure of ERK5 in complex with an MKK5 construct comprised of the PB1 domain and the linear binding motif. We show that ERK5 has distinct protein-protein interaction surfaces compared with ERK2, which is the closest ERK5 paralog. The two MAPKs have characteristically different physiological functions and their distinct protein-protein interaction surface topography enables them to bind different sets of activators and substrates. Structural and biochemical characterization revealed that the MKK5 PB1 domain cooperates with the MAPK binding linear motif to achieve substrate specific binding, and it also enables co-recruitment of the upstream activating enzyme and the downstream substrate into one signaling competent complex. Studies on present day MAPKs and MKKs hint on the way protein kinase networks may evolve. In particular, they suggest how paralogous enzymes with similar catalytic properties could acquire novel signaling roles by merely changing the way they make physical links to other proteins.

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Organizational Affiliation: 

Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 7	A, B	442	Homo sapiens	Mutation(s): 0  Gene Names: MAPK7, BMK1, ERK5, PRKM7 EC: 2.7.11.24
Find proteins for Q13164 (Homo sapiens) Explore Q13164  Go to UniProtKB:  Q13164
NIH Common Fund Data Resources
PHAROS  Q13164 GTEx  ENSG00000166484

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.290 
• R-Value Work: 0.262 
• R-Value Observed: 0.263 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.9	α = 90
b = 93.22	β = 89.96
c = 69.26	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-10 
• Released Date: 2013-02-13 
Deposition Author(s): Gogl, G., Remenyi, A.

Revision History 

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Database references