5OXI

C-terminally retracted ubiquitin L67S mutant

Summary for 5OXI

• Entry DOI: 10.2210/pdb5oxi/pdb
• Descriptor: Ubiquitin L67S mutant, SULFATE ION (3 entities in total)
• Functional Keywords: ubiquitin, post-translational modifier, signaling protein
• Biological source: Homo sapiens (Human)
• Cellular location: Ubiquitin: Cytoplasm : P0CG48
• Total number of polymer chains: 2
• Total formula weight: 17677.88

Authors

Gladkova, C.G.,Schubert, A.F.,Wagstaff, J.L.,Pruneda, J.N.,Freund, S.M.V.,Komander, D. (deposition date: 2017-09-06, release date: 2017-11-22, Last modification date: 2024-01-17)

Primary citation

Gladkova, C.,Schubert, A.F.,Wagstaff, J.L.,Pruneda, J.N.,Freund, S.M.,Komander, D.
An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1.
EMBO J., 36:3555-3572, 2017

PubMed Abstract: The Ser/Thr protein kinase PINK1 phosphorylates the well-folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic equilibrium between the known, common Ub conformation and a distinct, second conformation wherein the last β-strand is retracted to extend the Ser65 loop and shorten the C-terminal tail. We show using chemical exchange saturation transfer (CEST) nuclear magnetic resonance experiments that a similar, C-terminally retracted (Ub-CR) conformation also exists at low population in wild-type Ub. Point mutations in the moving β5 and neighbouring β-strands shift the Ub/Ub-CR equilibrium. This enabled functional studies of the two states, and we show that while the Ub-CR conformation is defective for conjugation, it demonstrates improved binding to PINK1 through its extended Ser65 loop, and is a superior PINK1 substrate. Together our data suggest that PINK1 utilises a lowly populated yet more suitable Ub-CR conformation of Ub for efficient phosphorylation. Our findings could be relevant for many kinases that phosphorylate residues in folded protein domains.

PubMed: 29133469
DOI: 10.15252/embj.201797876

Experimental method

X-RAY DIFFRACTION (1.63 Å)