1UKI

Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125

Heo, Y.-S.Kim, S.K.Seo, C.I.Kim, Y.K.Sung, B.-J.Lee, H.S.Lee, J.I.Park, S.-Y.Kim, J.H.Hwang, K.Y.Hyun, Y.-L.Jeon, Y.H.Ro, S.Cho, J.M.Lee, T.G.Yang, C.-H.

(2004) Embo J. 23: 2185-2195

  • DOI: 10.1038/sj.emboj.7600212
  • Primary Citation of Related Structures:  1UKH

  • PubMed Abstract: 
  • The c-jun N-terminal kinase (JNK) signaling pathway is regulated by JNK-interacting protein-1 (JIP1), which is a scaffolding protein assembling the components of the JNK cascade. Overexpression of JIP1 deactivates the JNK pathway selectively by cytop ...

    The c-jun N-terminal kinase (JNK) signaling pathway is regulated by JNK-interacting protein-1 (JIP1), which is a scaffolding protein assembling the components of the JNK cascade. Overexpression of JIP1 deactivates the JNK pathway selectively by cytoplasmic retention of JNK and thereby inhibits gene expression mediated by JNK, which occurs in the nucleus. Here, we report the crystal structure of human JNK1 complexed with pepJIP1, the peptide fragment of JIP1, revealing its selectivity for JNK1 over other MAPKs and the allosteric inhibition mechanism. The van der Waals contacts by the three residues (Pro157, Leu160, and Leu162) of pepJIP1 and the hydrogen bonding between Glu329 of JNK1 and Arg156 of pepJIP1 are critical for the selective binding. Binding of the peptide also induces a hinge motion between the N- and C-terminal domains of JNK1 and distorts the ATP-binding cleft, reducing the affinity of the kinase for ATP. In addition, we also determined the ternary complex structure of pepJIP1-bound JNK1 complexed with SP600125, an ATP-competitive inhibitor of JNK, providing the basis for the JNK specificity of the compound.


    Organizational Affiliation

    The Division of Drug Discovery, CrystalGenomics, Inc., Daeduk Biocommunity, Jeonmin-dong, Daejon, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mitogen-activated protein kinase 8 isoform 4
A
369Homo sapiensGene Names: MAPK8 (JNK1, PRKM8, SAPK1, SAPK1C)
EC: 2.7.11.24
Find proteins for P45983 (Homo sapiens)
Go to Gene View: MAPK8
Go to UniProtKB:  P45983
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
11-mer peptide from C-jun-amino-terminal kinase interacting protein 1
B
11Mus musculusGene Names: Mapk8ip1 (Ib1, Jip1, Mapk8ip, Prkm8ip)
Find proteins for Q9WVI9 (Mus musculus)
Go to UniProtKB:  Q9WVI9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
537
Query on 537

Download SDF File 
Download CCD File 
A
2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE
C14 H8 N2 O
ACPOUJIDANTYHO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
537IC50: 40 - 14000 nM (85) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.697α = 90.00
b = 79.460β = 90.00
c = 82.860γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance