6OPK image
Deposition Date 2019-04-25
Release Date 2019-07-31
Last Version Date 2024-11-20
Entry Detail
PDB ID:
6OPK
Keywords:
Title:
Phosphorylated ERK2 with Vertex-11e
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.54 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Mitogen-activated protein kinase 1
Gene (Uniprot):Mapk1
Chain IDs:A
Chain Length:352
Number of Molecules:1
Biological Source:Rattus norvegicus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PTR A TYR modified residue
TPO A THR modified residue
Ligand Molecules
Primary Citation
Activation loop dynamics are controlled by conformation-selective inhibitors of ERK2.
Proc.Natl.Acad.Sci.USA 116 15463 15468 (2019)
PMID: 31311868 DOI: 10.1073/pnas.1906824116

Abstact

Conformational selection by small molecules expands inhibitory possibilities for protein kinases. Nuclear magnetic resonance (NMR) measurements of the mitogen-activated protein (MAP) kinase ERK2 have shown that activation by dual phosphorylation induces global motions involving exchange between two states, L and R. We show that ERK inhibitors Vertex-11e and SCH772984 exploit the small energetic difference between L and R to shift the equilibrium in opposing directions. An X-ray structure of active 2P-ERK2 complexed with AMP-PNP reveals a shift in the Gly-rich loop along with domain closure to position the nucleotide in a more catalytically productive conformation relative to inactive 0P-ERK2:ATP. X-ray structures of 2P-ERK2 complexed with Vertex-11e or GDC-0994 recapitulate this closure, which is blocked in a complex with a SCH772984 analog. Thus, the L→R shift in 2P-ERK2 is associated with movements needed to form a competent active site. Solution measurements by hydrogen-exchange mass spectrometry (HX-MS) reveal distinct binding interactions for Vertex-11e, GDC-0994, and AMP-PNP with active vs. inactive ERK2, where the extent of HX protection correlates with R state formation. Furthermore, Vertex-11e and SCH772984 show opposite effects on HX near the activation loop. Consequently, these inhibitors differentially affect MAP kinase phosphatase activity toward 2P-ERK2. We conclude that global motions in ERK2 reflect conformational changes at the active site that promote productive nucleotide binding and couple with changes at the activation loop to allow control of dephosphorylation by conformationally selective inhibitors.

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Primary Citation of related structures