Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Biology

Background:

• RNF4 is an E3 ubiquitin ligase that targets poly-SUMO-modified proteins for degradation.
• RNF4 possesses four tandem SUMO-interaction motifs (SIMs) for selective protein binding.
• SUMOylation is a critical post-translational modification regulating various cellular processes.

Purpose of the Study:

• To structurally and functionally characterize the interaction between the RNF4-SIMs domain and tetra-SUMO2 chains.
• To elucidate the binding mechanism and affinity of individual SIM repeats to SUMO2.
• To determine the overall complex structure formed by RNF4-SIMs and tetra-SUMO2.

Main Methods:

• Multi-faceted biochemical and biophysical approaches were employed.
• Small-angle X-ray scattering (SAXS) was used to study the complex in solution.
• High-accuracy, low-resolution, de novo (HADDOCK) modeling was utilized for structural prediction.

Main Results:

• The RNF4-SIMs domain and SUMO2 linkers are intrinsically disordered in solution.
• SIM2 and SIM3 of RNF4 exhibit high-affinity binding to SUMO2, forming the primary recognition module.
• The RNF4-SIMs domain binds antiparallel to the tetra-SUMO2 chain, forming an ordered, superhelical complex.

Conclusions:

• The RNF4-SIMs domain exhibits a unique binding mode to tetra-SUMO2 chains, wrapping around the SUMO protamers.
• This ordered complex formation is essential for RNF4's function in targeting SUMOylated proteins for degradation.
• The study provides structural insights into the recognition and binding of poly-SUMOylated substrates by E3 ligases.