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

• Published in: Biochemical journal Vol. 462; no. 1; p. 53
• Main Authors: Kung, Camy C-H, Naik, Mandar T, Wang, Szu-Huan, Shih, Hsiu-Ming, Chang, Che-Chang, Lin, Li-Ying, Chen, Chia-Lin, Ma, Che, Chang, Chi-Fon, Huang, Tai-Huang
• Format: Journal Article
• Language: English
• Published: England 15.08.2014
• Subjects: Amino Acid Motifs - physiology; Nuclear Magnetic Resonance, Biomolecular; Nuclear Proteins - metabolism; Protein Binding; Protein Structure, Tertiary; Scattering, Small Angle; Small Ubiquitin-Related Modifier Proteins - metabolism; Transcription Factors - metabolism; Ubiquitin-Protein Ligases - metabolism; X-Ray Diffraction
• ISSN: 1470-8728
• DOI: 10.1042/bj20140521

The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.