Global sumoylation, SUMO chain formation, and genome stabilization are all 
outputs generated by a limited repertoire of enzymes. Mechanisms driving 
selectivity for each of these processes are largely uncharacterized. Here, 
through crystallographic analyses we show that the SUMO E2 Ubc9 forms a 
noncovalent complex with a SUMO-like domain of Rad60 (SLD2). Ubc9:SLD2 and 
Ubc9:SUMO noncovalent complexes are structurally analogous, suggesting that 
differential recruitment of Ubc9 by SUMO or Rad60 provides a novel means for 
such selectivity. Indeed, deconvoluting Ubc9 function by disrupting either the 
Ubc9:SLD2 or Ubc9:SUMO noncovalent complex reveals distinct roles in 
facilitating sumoylation. Ubc9:SLD2 acts in the Nse2 SUMO E3 ligase-dependent 
pathway for DNA repair, whereas Ubc9:SUMO instead promotes global sumoylation 
and chain formation, via the Pli1 E3 SUMO ligase. Moreover, this Pli1-dependent 
SUMO chain formation causes the genome instability phenotypes of SUMO-targeted 
ubiquitin ligase (STUbL) mutants. Overall, we determine that, unexpectedly, Ubc9 
noncovalent partner choice dictates the role of sumoylation in distinct cellular 
pathways.