Structural basis for SUMO‐E2 interaction revealed by a complex model using docking approach in combination with NMR data

Abstract

The interaction between small ubiquitin-related modifier SUMO and its conjugating-enzyme Ubc9 (E2) is an essential step in SUMO conjugation cascade. However, an experimental structure of such a transient complex is still unavailable. Here, a structural model of SUMO-3-Ubc9 complex was obtained with HADDOCK, combining NMR chemical shift mapping information. Docking calculations were performed using SUMO-3 and Ubc9 structures as input. The resulting complex reveals that the complementary surface electrostatic potentials contribute dominantly to the specific interaction. At the interface, similar numbers of oppositely-charged conserved residues are identified on the respective binding partners. Hydrogen bonds are formed in the vicinity of the interface to stabilize the complex. Comparison of the structure of SUMO-3-Ubc9 complex generated by HADDOCK and the experimental structures in free form indicates that SUMO-3 and Ubc9 maintain their respective fold as a whole after docking. However, the N-terminal helix alpha1 and its subsequent L1 loop of Ubc9 experience sizeable changes upon complex formation. They cooperatively move towards the hydrophilic side of the beta-sheet of SUMO-3. Our observations are consistent with the data from previous Ubc9 mutational analysis and conformational flexibility studies. Together, we have proposed that the SUMO-3-Ubc9 interaction is strongly electrostatically driven and the N terminus of Ubc9 shifts to SUMO-3 to facilitate the interaction. The NMR-based structural model, which provides considerable insights into the molecular basis of the specific SUMO-E2 recognition and interaction, implicates the general interaction mode between SUMO-3 and Ubc9 homologues from yeast to humans.

Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation

“…We have now shown the high‐resolution details of this interaction and found that SUMO interacts with the N‐terminal helix, the first β‐strand and the intervening loop of Ubc9. Recently, a model for the interaction between Ubc9 and SUMO3 was created by docking approaches in combination with NMR interaction data (Ding et al , 2005). In this model, the equivalent residues of SUMO3, compared to SUMO1 in our structure, interact with Ubc9.…”

Optimized grid‐based protein–protein docking as a global search tool followed by incorporating experimentally derivable restraints

“…Protein–protein docking refers to the prediction of the structures of protein complexes based on the structures of their constituting components, namely, receptors and ligands. One major difficulty associated with docking is that the conformational changes upon complex formation must be considered when only the structures of the separated receptor and ligand are known 1–5. For this purpose, both implicit and explicit approaches have been proposed 6.…”

Alternative splicing of the SUMO1/2/3 transcripts affects cellular SUMOylation and produces functionally distinct SUMO protein isoforms

“…The first, driven by the E1-SUMO complex, which mediates the transference of SUMO from the E1 to the E2 enzyme, appears dependent on residues Gln29, Arg63, Gln92, Gln94, Thr95, Gly96, and Gly97 in SUMO1, and residues Gln25, Arg59, Gln88, Gln90, Thr91, Gly92, and Gly93 in SUMO2. The second constitutes a non-covalent interaction that appears important for SUMO chain formation, and is mediated by residues Gln29, Glu33, Arg63, Leu65, Glu67, Gly81, Glu85, Asp86, Val87, Glu89, and Tyr91 in SUMO1, and Gln25, Val29, Arg59, Arg61, Asp63, Glu77, Glu81, Asp82, Thr83, Asp85, and Phe87 in SUMO2 [62][63][64][65] . Out of all the residues indicated to mediate some type of interaction with Ubc9, Gln29 is absent in SUMO1α while Arg59, Arg61, and Asp63 are absent in SUMO2α.…”