@kheewoongbaek.bsky.social

WE'RE HIRING! Thanks to some recent successes with NIH funding, we're seeking two new postdoctoral scholars to join our team. See below for details. Please share widely and feel free to reach out with any questions!

New year, new preprint! 🎊 We are excited to share our recent work on #E3 ligase regulation in #metabolism! www.biorxiv.org/content/10.6... #ubiquitin #targetedproteindegradation #chemicalbiology 1/6

A CK2-FBXW11 kinase-E3 ubiquitin ligase cascade is a metabolic sensor regulating Tryptophan 2,3-dioxygenase stability

Small molecules toggling the ubiquitin-proteasome system (UPS) are powerful regulators of protein degradation. Yet, mechanistic knowledge of how endogenous ligands gate UPS decisions remains rudimentary. Here, we define control of UPS access to Tryptophan-2,3-dioxygenase (TDO2), which converts the essential amino acid tryptophan (Trp) to N-formylkynurenine. When Trp concentrations are limiting, TDO2 is degraded to avert tryptophanemia. Using CRISPRi screening and biochemistry, we identify a CK2-FBXW11 kinase-E3 ligase cascade that generates and recognizes tandem TDO2 phosphodegrons when not protected by Trp. Trp binding to an exosite safeguards TDO2 from phosphorylation-dependent ubiquitylation. Effects of Trp analogs on CK2-FBXW11-dependent ubiquitylation indicated that the indole, amino, and carboxylate groups are necessary for substrate shielding. Cryo-EM reveals how these moieties order a region proximal to the phosphodegrons; without Trp, this segment is flexible, enabling phosphorylation-coupled ubiquitylation. Overall, our data uncovered an endogenous small molecule allosterically stabilizing its own metabolizing enzyme through protection from a phosphorylation-ubiquitylation cascade. ### Competing Interest Statement B.A.S. is a member of the scientific advisory boards of Proxygen and Lyterian. The other authors declare no competing interests. Max Planck Society, https://ror.org/01hhn8329 European Union, ERC AdvG, UPSmeetMet, 101098161 to BAS Boehringer Ingelheim Fonds, https://ror.org/00dkye506

biorxiv.org

📢 Save the Date! The next FREE Dana-Farber TPD In-Person Event is coming soon! Join us for an afternoon of cutting-edge science, networking, and community building focused on Targeted Protein Degradation (TPD). Stay tuned for registration and speaker details.

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Super excited to share our latest work on deciphering the #Ubiquitin Code “𝗨𝗯𝗶𝗥𝗘𝗔𝗗 𝗱𝗲𝗰𝗶𝗽𝗵𝗲𝗿𝘀 𝗽𝗿𝗼𝘁𝗲𝗮𝘀𝗼𝗺𝗮𝗹 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗰𝗼𝗱𝗲 𝗼𝗳 𝗵𝗼𝗺𝗼𝘁𝘆𝗽𝗶𝗰 𝗮𝗻𝗱 𝗯𝗿𝗮𝗻𝗰𝗵𝗲𝗱 𝗞48 𝗮𝗻𝗱 𝗞63 𝘂𝗯𝗶𝗾𝘂𝗶𝘁𝗶𝗻 𝗰𝗵𝗮𝗶𝗻𝘀” @cp-molcell.bsky.social 1/8 www.cell.com/molecular-ce...

UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains

Ubiquitin chains determine the fates of their modified proteins, including proteasomal degradation. Kiss et al. present UbiREAD, a technology to monitor cellular degradation and deubiquitination at hi...

cell.com

Extremely excited to be joining the vibrant community of the Vienna BioCenter to build up cryo-ET and cryo-FIB milling on campus soon!

IMP@impvienna.bsky.social · 2y ago

We will soon welcome @svenklumpe.bsky.social to the Vienna BioCenter, where he will use cryo-Electron Tomography to study - among other things - how #transposons shape #germlines. Sven's lab will be @imbavienna.bsky.social *AND* the IMP. Full story: www.viennabiocenter.org/about/news/s...

🎉Super excited to share our story on how the substrate receptor FBXO31 functions as a quality control factor by recognizing amides. This has been an amazing collaboration between Bode lab and @jcornlab.bsky.social. Special shutout goes to @matthiasmuhar.bsky.social www.nature.com/articles/s41...

C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature

SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.

nature.com