Proline is one of the abundant amino acids in grape must, but in winemaking processes it is poorly assimilated by the yeast Saccharomyces cerevisiae. This often causes a nitrogen deficiency during fermentation and proline accumulation in wine. Our previous study showed that arginine inhibits proline utilization by specifically inducing the endocytosis of the high-affinity proline transporter Put4. However, the detailed mechanisms underlying this induction are still unclear. Here, we propose a possible mechanism mediated by the ubiquitin ligase Rsp5 and its adaptor protein, Art3. First, we found that the ubiquitination activity of Rsp5 was essential for the arginine-induced endocytosis of Put4. Because Put4 contains no Rsp5-binding motif, we next screened an adaptor protein that plays a role in the arginine-induced endocytosis of Put4. Our genetic and biochemical analyses clearly revealed that the ART3 gene-disrupted cells were defective in Put4 endocytosis, indicating that Art3 is a key regulator for Put4 endocytosis. More importantly, we discovered that deletion of ART3 remarkably canceled the inhibitory effects of arginine on proline utilization. The present results could hold promise for the development of wine yeast strains that can efficiently assimilate the abundant proline in grape must during the fermentation processes.