Structural and mechanistic insights of GID E3 ubiquitin ligase
Thursday 27 October 2022
MRC Protein Phosphorylation and Ubiquitylation Spotlight Seminar
University of Dundee
Dundee DD1 5HL
Event location: MSI Small Lecture Theatre
Host: Dr. Yogesh Kulathu and Kirby Swatek
Event Speaker: Dawa Sherpa
Institution: PhD candidate Max Planck Institute of Biochemistry Munich
Dawafuti Sherpa was born and raised in Nepal. After finishing her early education in Kathmandu, she then moved to Munich, Germany. Here she obtained a Bachelor’s and Master’s degree from LMU (Ludwig Maximilians University) Munich. Dawa completed her Master’s thesis research in the lab of Brenda Schulman and then continued on as a PhD student. Currently she is in the final year of her PhD at the Max Planck Institute of Biochemistry, where her primary research focus is on understanding the mechanisms of E3 ubiquitin ligases.
E3 ubiquitin ligases have developed sophisticated strategies to specifically and efficiently target highly diverse ubiquitylation targets. Although there are numerous studies delineating mechanistic principles of ubiquitylation, little is known of how E3s are configured to match the quaternary structure of their substrates. Moreover, molecular and mechanistic insights into how a single E3 ubiquitin ligase can target a range of diverse substrates are still not fully understood. To address this, we set out to study the ubiquitin-mediated degradation of oligomeric gluconeogenic enzymes during recovery of yeast from glucose starvation. As discovered 20 years ago, degradation of several gluconeogenic enzymes is mediated by evolutionarily conserved multi-subunit E3 ubiquitin ligase called GID (Glucose Induced degradation Deficient). Our structural, biochemical and cellular data revealed supramolecular assembly of the GID E3, which is exquisitely tailored for targeting oligomeric nature of its gluconeogenic substrate fructose-1,6-bisphosphatase (Fbp1). To achieve such targeting, two catalytically active GID core complexes assemble into a remarkable 1.5 MDa oval structure – roughly the size of a 26S proteasome – accommodating the substrate in the middle. Such an arrangement promotes avid Fbp1 recruitment, simultaneous ubiquitylation of its multiple protomers and specific targeting of lysines nearby regions important for Fbp1 metabolic activity. Finally, we also demonstrated that the human ortholog of GID - the CTLH complex - reported previously to play a role in embryonic development, cell division and erythropoiesis, functions similarly as yeast GID and forms a variety of higher-order assemblies that can impart distinct functionalities.