Research ArticleStructural Biology

The apo-structure of the leucine sensor Sestrin2 is still elusive

Sci. Signal.  20 Sep 2016:
Vol. 9, Issue 446, pp. ra92
DOI: 10.1126/scisignal.aah4497

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An elusive apo-structure for Sestrin2

The protein complex called mTORC1 integrates growth factor signals and nutrient status to control cell growth and metabolism. The molecular mechanism by which mTORC1 activity is controlled by nutrients has been an active and controversial area of research. Castor1 and Sestrin2 have been reported to function as an arginine sensor and a leucine sensor, respectively. Saxton et al. provide evidence that all of the available Sestrin2 crystals and crystals that they generated in the absence of exogenous leucine contain a bound ligand that is most likely leucine. These data indicate that the unbound apo-structure awaits determination. Not only will a true apo-structure be informative, but crystals containing Sestrin2 and other binding partners will as well. Thus, the mechanism of exactly how amino acids control mTORC1 activity awaits further study.

Abstract

Sestrin2 is a GATOR2-interacting protein that directly binds leucine and is required for the inhibition of mTORC1 under leucine deprivation, indicating that it is a leucine sensor for the mTORC1 pathway. We recently reported the structure of Sestrin2 in complex with leucine [Protein Data Bank (PDB) ID, 5DJ4] and demonstrated that mutations in the leucine-binding pocket that alter the affinity of Sestrin2 for leucine result in a corresponding change in the leucine sensitivity of mTORC1 in cells. A lower resolution structure of human Sestrin2 (PDB ID, 5CUF), which was crystallized in the absence of exogenous leucine, showed Sestrin2 to be in a nearly identical conformation as the leucine-bound structure. On the basis of this observation, it has been argued that leucine binding does not affect the conformation of Sestrin2 and that Sestrin2 may not be a sensor for leucine. We show that simple analysis of the reported “apo”-Sestrin2 structure reveals the clear presence of prominent, unmodeled electron density in the leucine-binding pocket that exactly accommodates the leucine observed in the higher resolution structure. Refining the reported apo-structure with leucine eliminated the large Fobs-Fcalc difference density at this position and improved the working and free R factors of the model. Consistent with this result, our own structure of Sestrin2 crystallized in the absence of exogenous leucine also contained electron density that is best explained by leucine. Thus, the structure of apo-Sestrin2 remains elusive.

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