Structural basis studies of ubiquitin/sumo-related protease activity

• Autores: Ying Li
• Directores de la Tesis: David Reverter Cendrós (dir. tes.)
• Lectura: En la Universitat Autònoma de Barcelona ( España ) en 2022
• Idioma: inglés
• Tribunal Calificador de la Tesis: Francesc Xavier Gomis-Rüth (presid.), Bernat Crosas Navarro (secret.)
• Programa de doctorado: Programa de Doctorado en Bioquímica, Biología Molecular y Biomedicina por la Universidad Autónoma de Barcelona
• Materias:
  • Química
    • Bioquímica
• Enlaces
  • Tesis en acceso abierto en: TDX
• Resumen

  • Post-translational protein modifications by ubiquitin and SUMO regulate many major pathways in the cell. These modifications can be reversed by de-ubiquitinating enzymes such as ubiquitin-specific proteases (USPs) or deSUMOylaseas such as SUMO-specific proteases (SENPs). Proteolytic activity towards ubiquitin-modified substrates is common to all USP family members except for USPL1, which shows a unique preference for the small ubiquitin-like modifier SUMO. In humans, the deSUMOylating activity is mainly conducted by the SENP/ULP protease family, which is constituted of six members sharing a homologous catalytic globular domain. SENP6 and SENP7 are the most divergent members of the family and they show a unique SUMO2/3 isoform preference and a particular activity for dismantling polySUMO2 chains. NopD, an effector of the type III secretion system (T3SS) from Bradyrhizobium, is a multipurpose enzyme with specificity for ubiquitin and plant SUMO substrates.

    In the present thesis, we first present the crystal structure of USPL1 bound to SUMO2. We find that USPL1 lacks major structural elements present in all canonical USPs members such as the so-called blocking loops, which facilitate SUMO binding instead of ubiquitin. Second, we reveal the crystal structure of the catalytic domain of human SENP7 bound to SUMO2, and described the specific contacts between SUMO2 and a unique insertion in SENP7 (named Loop1) that is responsible for the SUMO2 isoform specificity. We finally present the crystal structures of NopD bound to AtSUMO2 and to ubiquitin, and reveal the molecular details for this dual activity of NopD for SUMO and ubiquitin. Mutagenesis analysis disclose the determinants, such as the unique insertion loop in NopD, that are responsible for unusual dual NopD activity for SUMO and ubiquitin.

    All results give insight into the structural details of these protein complexes' interface and contribute to enrich the knowledge of the distinct evolutionary directions followed by members of deubiquitinating and deSUMOylating families.