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

Thielen, A. S.; Bräuning, B.; Gottemukkala, K. V.; Müller, J.; Prabu, J. R.; Klaessens, S.; Van den Eynde, B.; Murray, P. J.; Schulman, B. A.

doi:10.64898/2026.01.12.698998

bioRxiv · 10.64898/2026.01.12.698998

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

Thielen, A. S.·Bräuning, B.·Gottemukkala, K. V.·Müller, J.·Prabu, J. R.·Klaessens, S.·Van den Eynde, B.·Murray, P. J.·Schulman, B. A.

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Abstract

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.

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Thielen, A. S., Bräuning, B., Gottemukkala, K. V., Müller, J., Prabu, J. R., Klaessens, S., Van den Eynde, B., Murray, P. J., Schulman, B. A.. 2026-01-12. A CK2-FBXW11 kinase-E3 ubiquitin ligase cascade is a metabolic sensor regulating Tryptophan 2,3-dioxygenase stability. https://doi.org/10.64898/2026.01.12.698998

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