4IC7

Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 7A,
B [auth D]
442Homo sapiensMutation(s): 0 
Gene Names: MAPK7BMK1ERK5PRKM7
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q13164 (Homo sapiens)
Explore Q13164 
Go to UniProtKB:  Q13164
PHAROS:  Q13164
GTEx:  ENSG00000166484 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13164
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 5C [auth E],
D [auth B]
126Homo sapiensMutation(s): 0 
Gene Names: MAP2K5MEK5MKK5PRKMK5
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13163 (Homo sapiens)
Explore Q13163 
Go to UniProtKB:  Q13163
PHAROS:  Q13163
GTEx:  ENSG00000137764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13163
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
E [auth A],
F [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.37α = 90
b = 69.37β = 90
c = 271.24γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations