Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.Kung, C.C.-H., Naik, M.T., Wang, S.H., Shih, H.M., Chang, C.C., Lin, L.Y., Chen, C.L., Ma, C., Chang, C.F., Huang, T.H.
(2014) Biochem J 462: 53-65
- PubMed: 24844634
- DOI: https://doi.org/10.1042/BJ20140521
- Primary Citation of Related Structures:
- PubMed Abstract:
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.
¶Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.