PXD053502-1

PXD053502 is an original dataset announced via ProteomeXchange.

Title	Mechanism of degrader-targeted protein ubiquitinability
Description	Small molecule degraders of disease-driving proteins offer a clinically proven modality with enhanced therapeutic efficacy and the potential to tackle previously undrugged targets. Thermodynamically stable and kinetically long-lived degrader-mediated ternary complexes can drive faster, more profound and durable target degradation, however the mechanistic features by which they impact on target ubiquitination remain elusive. Here, we solve cryo-EM structures of the VHL Cullin 2 RING E3 ligase complexed with degrader MZ1, target protein Brd4BD2 and primed for catalysis with its cognate E2-ubiquitin bound. We find that Brd4BD2 adopts a favourable orientation towards the E2 active site. Mass spectrometry illuminates a patch of favourably ubiquitinable lysines on one face of in vitro ubiquitinated Brd4BD2, with Lys456 showing optimal distance and geometry for nucleophilic attack highlighted by cryo-EM. In vitro ubiquitination coupled with cellular degradation and ubiquitinomics confirm the importance of Lys456 and the ‘ubiquitination zone’ lysines. Our results demonstrate the proficiency of MZ1 in directing the substrate towards catalysis, explains the favourability of Brd4BD2 for ubiquitination bu UBE2R1, and reveals the flexibility of the enzyme in capturing sub-optimal lysines. We propose a model for ubiquitinability of degrader-recruited targets that provides a mechanistic blueprint for further rational drug design and optimization.
HostingRepository	PRIDE
AnnounceDate	2024-11-08
AnnouncementXML	Submission_2024-11-08_03:22:34.818.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gajanan Sathe
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-28 14:47:41	ID requested
⏵ 1	2024-11-08 03:22:35	announced

Crowe C, Nakasone MA, Chandler S, Craigon C, Sathe G, Tatham MH, Makukhin N, Hay RT, Ciulli A, Mechanism of degrader-targeted protein ubiquitinability. Sci Adv, 10(41):eado6492(2024) [pubmed]

10.1126/sciadv.ado6492;

submitter keyword: MZ1,VHL, ubiquitination

Professor Alessio Ciulli
contact affiliation	Professor Alessio Ciulli Director Centre for Targeted Protein Degradation 1 James Lindsay Place Dundee DD1 5JJ
contact email	a.ciulli@dundee.ac.uk
lab head
Gajanan Sathe
contact affiliation	Centre for Targeted Protein Degradation (CeTPD) University of Dundee
contact email	gsathe001@dundee.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053502
     1. Label: PRIDE project
     2. Name: Mechanism of degrader-targeted protein ubiquitinability