4WZP

Ser65 phosphorylated ubiquitin, major conformation

Summary for 4WZP

• Entry DOI: 10.2210/pdb4wzp/pdb
• Related: 1ubq
• Descriptor: ubiquitin, SULFATE ION (3 entities in total)
• Functional Keywords: posttranslational modification, phosphorylation, mitophagy, parkin, pink1, signaling protein
• Biological source: Homo sapiens (Human)
• Cellular location: Ubiquitin: Cytoplasm : P0CG47
• Total number of polymer chains: 8
• Total formula weight: 69926.93

Authors

Wauer, T.,Wagstaff, J.,Freund, S.M.V.,Komander, D. (deposition date: 2014-11-20, release date: 2015-01-14, Last modification date: 2024-10-23)

Primary citation

Wauer, T.,Swatek, K.N.,Wagstaff, J.L.,Gladkova, C.,Pruneda, J.N.,Michel, M.A.,Gersch, M.,Johnson, C.M.,Freund, S.M.,Komander, D.
Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis.
Embo J., 34:307-325, 2015

PubMed Abstract: The protein kinase PINK1 was recently shown to phosphorylate ubiquitin (Ub) on Ser65, and phosphoUb activates the E3 ligase Parkin allosterically. Here, we show that PINK1 can phosphorylate every Ub in Ub chains. Moreover, Ser65 phosphorylation alters Ub structure, generating two conformations in solution. A crystal structure of the major conformation resembles Ub but has altered surface properties. NMR reveals a second phosphoUb conformation in which β5-strand slippage retracts the C-terminal tail by two residues into the Ub core. We further show that phosphoUb has no effect on E1-mediated E2 charging but can affect discharging of E2 enzymes to form polyUb chains. Notably, UBE2R1- (CDC34), UBE2N/UBE2V1- (UBC13/UEV1A), TRAF6- and HOIP-mediated chain assembly is inhibited by phosphoUb. While Lys63-linked poly-phosphoUb is recognized by the TAB2 NZF Ub binding domain (UBD), 10 out of 12 deubiquitinases (DUBs), including USP8, USP15 and USP30, are impaired in hydrolyzing phosphoUb chains. Hence, Ub phosphorylation has repercussions for ubiquitination and deubiquitination cascades beyond Parkin activation and may provide an independent layer of regulation in the Ub system.

PubMed: 25527291
DOI: 10.15252/embj.201489847

Experimental method

X-RAY DIFFRACTION (1.9 Å)