PDBsum entry 1ukh

Transferase

PDB id: 1ukh

Contents

Protein chain

321 a.a. *

Ligands

PRO-LYS-ARG-PRO-THR-THR-LEU-ASN-LEU-PHE

Waters ×95

* Residue conservation analysis

PDB id:

1ukh

Name:

Transferase

Title:

Structural basis for the selective inhibition of jnk1 by the scaffolding protein jip1 and sp600125

Structure:

Mitogen-activated protein kinase 8 isoform 4. Chain: a. Fragment: residues 1-369. Synonym: jnk1. Engineered: yes. 11-mer peptide from c-jun-amino-terminal kinase interacting protein 1. Chain: b. Synonym: jip1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence occurs peptide synthesis

Biol. unit:

Dimer (from PQS)

Resolution:

2.35Å R-factor: 0.226 R-free: 0.245

Authors:

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

Key ref:

Y.S.Heo et al. (2004). Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125. EMBO J, 23, 2185-2195. PubMed id: 15141161 DOI: 10.1038/sj.emboj.7600212

Date:

23-Aug-03 Release date: 30-Aug-04

Protein chain

P45983  (MK08_HUMAN) -  Mitogen-activated protein kinase 8 from Homo sapiens

Seq: 427 a.a.

Struc: 321 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.11.24 - mitogen-activated protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/sj.emboj.7600212

EMBO J 23:2185-2195 (2004)

PubMed id: 15141161

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

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

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 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.

Selected figure(s)

Figure 4.
Figure 4 Distortion of the ATP-binding site caused by interdomain rearrangement upon pepJIP1 binding. (A) Structural comparison between JNK3 (green) and pepJIP1-bound JNK1 (violet) when the C-terminal domains of the kinases are superimposed. The conformational differences of the N-terminal domains can be easily distinguished when the conventional view of kinases is rotated by 45° along the horizontal axis. The yellow circle indicates the interaction between the 1 helix and the phosphorylation loop in JNK3, but not existing in JNK1 complexed with pepJIP1. (B) Comparison of ATP-binding sites between the JNK1 -pepJIP1 (violet) and JNK3 -AMPPNP (green) complexes. The AMPPNP bound in JNK3 is shown in a ball-and-stick model. The residues of JNK3 involved in the hydrogen bonding with AMPPNP are labeled. The side chains of the residues in the glycine-rich loop including E75 and A74 of JNK3 are omitted for clarity because the backbone amide groups only are involved in the hydrogen bonds with the phosphate groups of AMPPNP. (C) The structural comparison of the residues crucial for the catalytic activity between the JNK1 -pepJIP1 (violet) and JNK3 -AMPPNP (green) complexes. The residues in JNK1 and JNK3 are labeled red and black, respectively. In (B, C), hydrogen bonds are indicated by dashed lines.

Figure 5.
Figure 5 The inhibited phosphorylation of MBP, the docking site-independent substrate, due to the reduced ATP binding affinity to JNK1 by pepJIP1 binding. (A, B) The binding affinities of ATP to JNK1 were measured by ITC when pepJIP1 was unbound (A) and bound (B) to JNK1. (C) Dose-dependent inhibition of the kinase activity of JNK1 by pepJIP1 using MBP as substrates. The mutated pepJIP1 used for control experiment has the sequence of RPKAATTANAF.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2185-2195) copyright 2004.

Figures were selected by an automated process.