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Contents 1 FKBP12-rapamycin binding domain of mTOR 1.1 Introduction 1.2 Structure of FRB 1.3 References

FKBP12-rapamycin binding domain of mTOR

FRB domain of mTOR (or 2NPU) is responsible for the binding of the inhibitory cyclic macrolide Rapamycin

Introduction

spinqualitylabelsall models Cartoon model of the FRB domain of mTOR: N-terminus: red, C-terminus: blue Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

As a member of the phosphatidylinositol kinase-related kinases (PIKK)* the mammalian targert of rapamycin (mTOR)* is a multi domain protein which is involved in the regulation of cell growth and is an important target of survival signals in cancer cells.

The sequence of the 2549 residues is highly conserved across eukaryotes (40-60% precent sequence identity). The protein consists of several functional domain.
At the N-terminus there are 12 HEAT* repeats followed by a central FAT* domain (residues 1513-1910), a FRB domain (residues 2015-2114) a serine-threonine kinase domain (residues 2181-2484) and a C-terminal FATC* domain (residues 2515-2549).

The FKBP12-rapamycin binding (FRB) domain mediates ligand-dependent regulation of the kinase domain by binding different molecules. FRB binds the inhibitory cyclic macroloide* rapamycin in complex with the small peptidyl-prolyl cis-trans isomerase FKBP12* leading to a decreased activity of the kinase domain. Due to its inhibitory effect rapamycin has been a widely used tool for studying mTOR.
FRB is also capable of binding the activator phosphatidic acid* and small molecules, for example amino acids like leucine. ^[1]

Structure of FRB

spinqualitylabelsall models Surface structure of FRB Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

The FRB domain is made up of an disordered domain (greenlink) and a four α-helices bundle joined by short loops (, , , ) (Leone et al., 2006). Helix 3 contains a of approximately 45° and its N-terminal half is largely disordered.

The surface structure reveals two main interaction sites, a shallow made up by helix 1 and helix 4 which is responsible for the binding of rapamycin (Choi et al. 1996) and between helix 2 and helix 3. This cleft contains charged and hydrophobic residues and is expected to function as a binding site for small molecules to regulate mTOR activity.

The binding sites for phosphatidic acid and rapamycin show significant suggesting that rapamycin inhibits kinase activity of mTOR by blocking access of the activator phosphatidic acid. The positive charged residue R2109 plays a key role in the binding of phosphatidic acid as it binds to the negetively charged phosphate group of phosphatidic acid.

References

1. ↑ Veverka V, Crabbe T, Bird I, Lennie G, Muskett FW, Taylor RJ, Carr MD. Structural characterization of the interaction of mTOR with phosphatidic acid and a novel class of inhibitor: compelling evidence for a central role of the FRB domain in small molecule-mediated regulation of mTOR. Oncogene. 2008 Jan 24;27(5):585-95. Epub 2007 Aug 6. PMID:17684489