Understanding the mechanisms of UFMylation

  • Joshua Peter

Student thesis: Doctoral ThesisDoctor of Philosophy


Ubiquitin-fold modifier 1 (UFM1) is one of the recently discovered members of the Ubiquitin-like protein (Ubl) family. With a similar three-dimensional structure to Ubiquitin, UFM1 is covalently conjugated to lysine residues on target proteins, by a process called UFMylation. Protein UFMylation is emerging as a novel protein quality control system with functions focused on ER (Endoplasmic Reticulum) Phagy and Ribosomal Quality Control (RQC). Central to this modification system is the E3 ligase UFL1(UFM1 E3 Ligase 1) which is responsible for the conjugation of UFM1 onto its key target proteins predominantly on the Ribosome and ER membrane. With almost a decade passed, the precise mechanism by which UFM1 is conjugated onto substrate proteins is not understood. Here, in my PhD, I focused on developing biochemical tools to systematically characterize the key players involved in the ligation of UFM1 onto substrate proteins. I discover that UFL1 is an inactive enzyme on its own and is tightly regulated by two of its prominent binding partners namely, UFBP1 and CDK5RAP3. I show that UFL1 binds to UFBP1 to form an active E3 ligase complex. CDK5RAP3, on the other hand, functions as a regulatory module whose interaction with UFL1/UFBP1 complex, results in inhibition of UFMylation in vitro. Further, we employ biophysical and structural tools such as Crosslinking Mass spectrometry and Cryo-EM to gain mechanistic insights into the regulation of this multiprotein E3 ligase complex.
Date of Award2022
Original languageEnglish
SupervisorYogesh Kulathu (Supervisor)


  • UFMylation
  • UFL1

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