Crystal structure of JNK3: a kinase implicated in neuronal apoptosis

Xie, Xiaoling; Gu, Yong; Fox, Ted; Coll, Joyce T; Fleming, Mark A; Markland, William; Caron, Paul R; Wilson, Keith P; Su, Michael S-S

doi:10.1016/s0969-2126(98)00100-2

Cited by 198Protein Kinase Regulation and GTPase SignalingProtein Structure and DynamicsEnzyme Structure and Function

Crystal structure of JNK3: a kinase implicated in neuronal apoptosis

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Xie, Xiaoling, Gu, Yong, Fox, Ted, Coll, Joyce T, Fleming, Mark A, Markland, William, Caron, Paul R, Wilson, Keith P +1 more·1998·Structure

DOI 10.1016/s0969-2126(98)00100-2

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Abstract

Background The c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein (MAP) kinase family, and regulate signal transduction in response to environmental stress. Activation and nuclear localization of JNK3, a neuronal-specific isoform of JNK, has been associated with hypoxic and ischemic damage of CA1 neurons in the hippocampus. Knockout mice lacking JNK3 showed reduced apoptosis of hippocampal neurons and reduced seizure induced by kainic acid, a glutamate-receptor agonist. Thus, JNK3 may be important in the pathology of neurological disorders and is of significant medical interest.Results We report here the structure of unphosphorylated JNK3 in complex with adenylyl imidodiphosphate, an ATP analog. JNK3 has a typical kinase fold, with the ATP-binding site situated within a cleft between the N- and C-terminal domains. In contrast to other known MAP kinase structures, the ATP-binding site of JNK3 is well ordered; the glycine-rich nucleotide-binding sequence forms a beta-strand-turn-beta-strand structure over the nucleotide. Unphosphorylated JNK3 assumes an open conformation, in which the N- and C-terminal domains are twisted apart relative to their positions in cAMP-dependent protein kinase. The rotation leads to the misalignment of some of the catalytic residues. The phosphorylation lip of JNK3 partially blocks the substrate-binding site.Conclusions This is the first JNK structure to be determined, providing a unique opportunity to compare structures from the three MAP kinase subfamilies. The structure reveals atomic-level details of the shape of JNK3 and the interactions between the kinase and the nucleotide. The misalignment of catalytic residues and occlusion of the active site by the phosphorylation lip may account for the low activity of unphosphorylated JNK3. The structure provides a framework for understanding the substrate specificity of different JNK isoforms, and should aid the design of selective JNK3 inhibitors.

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The overall architecture of JNK1 is substantially equal to that of JNK3 due to 92% sequence identity.
“As a result of the high homology of sequences with 92% identity, the overall architecture of JNK1 is substantially equal to that of JNK3 (PDB entry 1JNK; Xie et al , 1998).”
From Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125 (2004) · cites this paper as Xie et al , 1998
Refolding of the phosphorylation loop is required to relieve steric constraints to substrate binding and activation of the substrate by JNK3.
“This structural feature of JNK3 suggests that refolding of this loop is required to relieve steric constraints to the substrate binding and the activation of the substrate by JNK3 (Xie et al , 1998).”
From Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125 (2004) · cites this paper as Xie et al , 1998

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Authors: Xie, X., Gu, Y., Fox, T., Coll, J. T., Fleming, M. A., Markland, W., Caron, P. R., Wilson, K. P., & Su, M. S.-S.
Affiliations: Vertex Pharmaceuticals (United States) (US)
Corresponding author: Xie, Xiaoling
Su, Michael S-S
ORCID: Xie, Xiaoling
Gu, Yong
Fleming, Mark A
Su, Michael S-S
Venue: Structure
Publisher: Elsevier BV
Published: 1998-08
Volume: 6
Issue: 8
Pages: 983-991
ISSN: 0969-2126 (ISSN-L)
DOI: 10.1016/s0969-2126(98)00100-2
OpenAlex: W2103381809
Cited by: 198
References: 39
Citations by year: 2026: 4 · 2025: 6 · 2024: 8 · 2023: 1 · 2022: 5 · 2021: 3 · 2020: 6 · 2019: 3 · 2018: 4 · 2017: 2 · 2016: 6 · 2015: 7 · 2014: 6 · 2013: 4 · 2012: 10
FWCI: 3.37
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 5464 d)
Locations: Structure (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords: JNK3, c-Jun N-terminal kinase, mitogen-activated protein kinase, kinase crystal structure, ATP binding site, catalytic residues, substrate specificity, neuronal apoptosis, hippocampal neurons, JNK3 inhibitors
MeSH terms: Adenylyl Imidodiphosphate, Amino Acid Sequence, Binding Sites, Models, Molecular, Molecular Sequence Data, Nerve Tissue Proteins, Phosphorylation, Protein Kinases, Protein-Tyrosine Kinases, Sequence Alignment, Apoptosis, Protein Serine-Threonine Kinases, Protein Structure, Secondary, Protein Folding, Calcium-Calmodulin-Dependent Protein Kinases, Crystallography, X-Ray, Mitogen-Activated Protein Kinases, Mitogen-Activated Protein Kinase 10

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Crystal structure of JNK3: a kinase implicated in neuronal apoptosis

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