Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation

Rachel M Jansen; Roberta Peruzzo; Simon A Fromm; Adam L Yokom; Roberto Zoncu; James H Hurley

doi:10.1126/sciadv.add2926

Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation

Sci Adv. 2022 Sep 16;8(37):eadd2926. doi: 10.1126/sciadv.add2926. Epub 2022 Sep 14.

Authors

Rachel M Jansen^{1

2}, Roberta Peruzzo¹, Simon A Fromm^{1

2}, Adam L Yokom^{1

2}, Roberto Zoncu^{1

2}, James H Hurley^{1

2

3}

Affiliations

¹ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
² California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
³ Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.

Abstract

The mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and catabolism in response to nutrients through phosphorylation of key substrates. The tumor suppressor folliculin (FLCN) is a RagC/D guanosine triphosphatase (GTPase)-activating protein (GAP) that regulates mTORC1 phosphorylation of MiT-TFE transcription factors, controlling lysosome biogenesis and autophagy. We determined the cryo-electron microscopy structure of the active FLCN complex (AFC) containing FLCN, FNIP2, the N-terminal tail of SLC38A9, the RagA^GDP:RagC^GDP.BeFx- GTPase dimer, and the Ragulator scaffold. Relative to the inactive lysosomal FLCN complex structure, FLCN reorients by 90°, breaks contact with RagA, and makes previously unseen contacts with RagC that position its Arg¹⁶⁴ finger for catalysis. Disruption of the AFC-specific interfaces of FLCN and FNIP2 with RagC eliminated GAP activity and led to nuclear retention of TFE3, with no effect on mTORC1 substrates S6K or 4E-BP1. The structure provides a basis for regulation of an mTORC1 substrate-specific pathway and a roadmap to discover MiT-TFE family selective mTORC1 antagonists.

Grants and funding

R01 GM111730/GM/NIGMS NIH HHS/United States