5T0N image
Entry Detail
PDB ID:
5T0N
Title:
Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2016-08-16
Release Date:
2016-10-05
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
I 2 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Sestrin-2
Chain IDs:A, B, C, D, E
Chain Length:480
Number of Molecules:5
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
The apo-structure of the leucine sensor Sestrin2 is still elusive.
Sci.Signal. 9 ra92 ra92 (2016)
PMID: 27649739 DOI: 10.1126/scisignal.aah4497

Abstact

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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Primary Citation of related structures