Crystal structure of the human Tip41 orthologue, TIPRL, reveals a novel fold and a binding site for the PP2Ac C-terminus

Abstract

TOR signaling pathway regulator-like (TIPRL) is a regulatory protein which inhibits the catalytic subunits of Type 2A phosphatases. Several cellular contexts have been proposed for TIPRL, such as regulation of mTOR signaling, inhibition of apoptosis and biogenesis and recycling of PP2A, however, the underlying molecular mechanism is still poorly understood. We have solved the crystal structure of human TIPRL at 2.15 Å resolution. The structure is a novel fold organized around a central core of antiparallel beta-sheet, showing an N-terminal α/β region at one of its surfaces and a conserved cleft at the opposite surface. Inside this cleft, we found a peptide derived from TEV-mediated cleavage of the affinity tag. We show by mutagenesis, pulldown and hydrogen/deuterium exchange mass spectrometry that this peptide is a mimic for the conserved C-terminal tail of PP2A, an important region of the phosphatase which regulates holoenzyme assembly, and TIPRL preferentially binds the unmodified version of the PP2A-tail mimetic peptide DYFL compared to its tyrosine-phosphorylated version. A docking model of the TIPRL-PP2Ac complex suggests that TIPRL blocks the phosphatase’s active site, providing a structural framework for the function of TIPRL in PP2A inhibition.

The PP2A‐interactor TIP41 modulates ABA responses in Arabidopsis thaliana

“…, best match LOC102597299 of the genome), encoding a TIP41‐like family protein, was shown to be specifically downregulated in potato cells adapted to high concentrations of PEG, used to induce osmotic stress (Ambrosone et al ., ). To functionally analyse the role of TIP41 in abiotic stress responses, we selected the Arabidopsis TIP41 orthologue At4g34270 (Scorsato et al ., ; Figure a). As indicated by the alignment of the deduced amino acid sequence of Arabidopsis TIP41 with orthologues from S. cerevisiae and Homo sapiens , as well as from Oryza sativa and Solanum tuberosum , a high degree of conservation indicates that the function of TIP41 might be conserved among eukaryotes (Figure a).…”

Structural basis for the disaggregase activity and regulation of Hsp104

“…As reported recently, the number of distinct Lys-Lys cross-links determined in a comparative XL-MS analysis is useful to estimate protein dynamics in a semi-quantitative manner (Scorsato et al, 2016; Walzthoeni et al, 2015). Accordingly, we reasoned that a structurally flexible Hsp104 particle that comprises a mixture of different conformations should yield a more complex cross-linking pattern than an Hsp104 variant that is closely embraced by a MD ring.…”

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi‐automated metrics

“…We note several cases of extremely difficult targets that classify as new folds with no reasonable predictions, for which the best models have very low GDTTS. Among them, extreme cases shown in Figure are an integral membrane STRA6 receptor for a retinol‐binding protein (split into T0863D1 and T0863D2, PDB ID 5sy1), a protein involved in regulation of mTOR signaling (T0864D1, PDB ID 5d9g), a protein with a cavity made up of a long twisted β‐sheet and four α‐helices with two additional long helices sticking out whose function remained undisclosed (T0923D1), a protein consisting in a long β‐sheet packed with shorter β‐sheets and α‐helices and a large fraction of loops, whose function also remained confidential (T0941D1). Additional new folds that displayed slightly higher average server performance levels include the α complex topology T0914D1, the α + β complex topology T0914D2, and the α bundle T0898D1.…”