5NG3

Structure of inactive kinase RIP2K(K47R)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of the inactive and active states of RIP2 kinase inform on the mechanism of activation.

Pellegrini, E.Signor, L.Singh, S.Boeri Erba, E.Cusack, S.

(2017) PLoS ONE 12: e0177161-e0177161

  • DOI: 10.1371/journal.pone.0177161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Innate immune receptors NOD1 and NOD2 are activated by bacterial peptidoglycans leading to recruitment of adaptor kinase RIP2, which, upon phosphorylation and ubiquitination, becomes a scaffold for downstream effectors. The kinase domain (RIP2K) is a ...

    Innate immune receptors NOD1 and NOD2 are activated by bacterial peptidoglycans leading to recruitment of adaptor kinase RIP2, which, upon phosphorylation and ubiquitination, becomes a scaffold for downstream effectors. The kinase domain (RIP2K) is a pharmaceutical target for inflammatory diseases caused by aberrant NOD2-RIP2 signalling. Although structures of active RIP2K in complex with inhibitors have been reported, the mechanism of RIP2K activation remains to be elucidated. Here we analyse RIP2K activation by combining crystal structures of the active and inactive states with mass spectrometric characterization of their phosphorylation profiles. The active state has Helix αC inwardly displaced and the phosphorylated Activation Segment (AS) disordered, whilst in the inactive state Helix αC is outwardly displaced and packed against the helical, non-phosphorylated AS. Biophysical measurements show that the active state is a stable dimer whilst the inactive kinase is in a monomer-dimer equilibrium, consistent with the observed structural differences at the dimer interface. We conclude that RIP2 kinase auto-phosphorylation is intimately coupled to dimerization, similar to the case of BRAF. Our results will help drug design efforts targeting RIP2 as a potential treatment for NOD2-RIP2 related inflammatory diseases.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-interacting serine/threonine-protein kinase 2
D, A
304Homo sapiensMutation(s): 1 
Gene Names: RIPK2 (CARDIAK, RICK, RIP2)
EC: 2.7.11.1
Find proteins for O43353 (Homo sapiens)
Go to Gene View: RIPK2
Go to UniProtKB:  O43353
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Receptor-interacting serine/threonine-protein kinase 2
B, C
304Homo sapiensMutation(s): 1 
Gene Names: RIPK2 (CARDIAK, RICK, RIP2)
EC: 2.7.11.1
Find proteins for O43353 (Homo sapiens)
Go to Gene View: RIPK2
Go to UniProtKB:  O43353
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.022α = 90.00
b = 103.310β = 90.00
c = 204.299γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Advisory, Data collection, Derived calculations, Refinement description