Edited by Thomas SöllnerThe Rab family of small GTPases functions in multiple aspects of cellular membrane trafficking. Proteins bearing a differentially expressed in normal and neoplastic cells (DENN) domain have emerged as the largest family of Rab-activating guanine nucleotide exchange factors (GEFs). Rab12 functions in the initiation of starvation-induced autophagy, and our previous work revealed that its activator, DENN domain-containing protein 3 (DENND3), is phosphorylated and activated upon starvation. However, how the GEF activity of DENND3 toward Rab12 is regulated at the molecular level is still not understood. Here, we combine size-exclusion chromatography, Förster resonance energy transfer, pulldown, and in vitro GEF assays to demonstrate that regulation of GEF activity is achieved through an intramolecular interaction that is controlled by a key residue in DENND3, tyrosine 940. Our study sheds light on the regulation of Rab12 activation and lays the groundwork for characterizing the regulation of other DENN domain-containing proteins.The Rab family of small GTPases functions in all aspects of cellular membrane trafficking ranging from vesicle budding to transport along the cytoskeleton and fusion with acceptor membranes. Rabs switch between an inactive GDP-bound form and an active GTP-bound form that interacts with effectors to mediate trafficking functions. Guanine nucleotide exchange factors (GEFs) 3 activate Rabs by facilitating the exchange of GDP for GTP (1). There are at least four families of GEFs for Rabs: TRAPP, Rabin8/Sec2, Vps9 domain-containing proteins, and DENN domain-containing proteins (2). With 26 distinct members, DENN domain-containing proteins are the largest family of Rab GEFs (3-8). They are involved in diverse biological functions (4), and mutations in several DENN domain-bearing proteins are linked to human diseases, including the tumor suppressor folliculin associated with Birt-HoggDubé syndrome (9), C9orf72 linked to familial frontotemporal dementia and amyotrophic lateral sclerosis (10, 11), and DENND1B associated with childhood asthma (12).We recently demonstrated that DENN domain-containing protein 3 (DENND3) functions in starvation-induced macroautophagy (13,14). Macroautophagy, which we will hereafter refer to as autophagy, is a conserved cellular process in which various physiological signals, including nutrient starvation, lead to the recruitment of organelles or cytosolic proteins into double membrane vesicles called autophagosomes. The autophagosomes eventually fuse with lysosomes for degradation of the internalized cargo. The resulting building blocks, such as amino acids, are then released back to the cytosol for reuse, helping cells survive starvation. Unc-51-like kinase (ULK) is the most upstream kinase for autophagy initiation (15). Upon starvation, ULK phosphorylates DENND3 at Ser-554 and Ser-572, recruiting the adapter protein 14-3-3, and this process leads to up-regulation of DENND3 GEF activity toward its substrate Rab12. Rab12 on recycling endosomes (1...