Structures and Functions of the Human GATOR1 Complex

Abstract

Eukaryotic cells coordinate available nutrients with their growth through the mechanistic target of rapamycin complex 1 (mTORC1) pathway, in which numerous evolutionarily conserved protein complexes survey and transmit nutrient inputs toward mTORC1. mTORC1 integrates these inputs and activates downstream anabolic or catabolic programs that are in tune with cellular needs, effectively maintaining metabolic homeostasis. The GAP activity toward Rags-1 (GATOR1) protein complex is a critical negative regulator of the mTORC1 pathway and, in the absence of amino acid inputs, is activated to turn off mTORC1 signaling. GATOR1-mediated inhibition of mTORC1 signaling is tightly regulated by an ensemble of protein complexes that antagonize or promote its activity in response to the cellular nutrient environment. Structural, biochemical, and biophysical studies of the GATOR1 complex and its interactors have advanced our understanding of how it regulates cellular metabolism when amino acids are limited. Here, we review the current research with a focus on GATOR1 structure, its enzymatic mechanism, and the growing group of proteins that regulate its activity. Finally, we discuss the implication of GATOR1 dysregulation in physiology and human diseases.

Keywords: Enzyme mechanism; GATOR1; GTPase activating protein (GAP); Protein structure; Rag GTPases; mTORC1.

Figure 1.

Overview of the mTORC1 signaling pathway. Selected protein components of the mTORC1 pathway are shown, focusing on the GATOR1 complex, its downstream effectors, and its upstream regulators. Amino acid sensors either directly modulate the activity of GATOR1, such as SAMTOR, or through GATOR2, such as Sestrin2 and Castor1.

Figure 2.

Architecture of the human GATOR1 complex. GATOR1 is a heterotrimeric protein complex consisting of DEPDC5 (green), NPRL2 (yellow), and NPRL3 (brown). The domain arrangements for each subunit are shown accordingly.

Figure 3.

Interaction between the GATOR1 subunits. (A) NPRL2-NPRL3 interactions. NPRL2 (yellow) and NPRL3 (brown) form extensive interactions through three pairs of domains, Longin-Longin, CTD-CTD, and CTD-INT. (B) DEPDC5-NPRL2 interactions. DEPDC5 (green) utilizes the four loops (loop A-loop D) to form redundant interactions with NPRL2 (yellow).

Figure 4.

GATOR1 contacts the Rag GTPase heterodimer via two modes. (A) Two binding sites on GATOR1 can be occupied by the Rag GTPase heterodimer: an inhibitory mode mediated by the critical strip (red) on DEPDC5, and a GAP mode mediated by the Arg78 residue on NPRL2. The catalytic finger of NPRL2 stimulates GTP hydrolysis by RagA only in the GAP mode. (B) GATOR1-Rag interaction in the inhibitory mode. The critical strip (red, a.a. 770–777 of DEPDC5) contacts the nucleotide binding pocket of RagA (pink). GDP:AlF₃ is a non-hydrolyzable GTP analog used to stabilize the complex. (C) GATOR1-Rag interaction in the GAP mode. Arg78 of NPRL2 inserts into the nucleotide binding pocket of RagA and points towards the β- and γ-phosphate of the bound nucleotide to stimulate GTP hydrolysis.