Structural insight into TIPE1 functioning as a lipid transfer protein

Abstract

As a member of the tumor necrosis factor-α-induced protein 8 (TNFAIP8/TIPE) family, TIPE1 has been found to be associated with many cellular signaling pathways in regulating apoptosis, autophagy, and tumorigenesis. However, the position of TIPE1 in the signaling network remains elusive. Here we present the crystal structure of zebrafish TIPE1 in complex with phosphatidylethanolamine (PE) at a resolution of 1.38 Å. By comparison with structures of other three TIPE family proteins, a universal phospholipid-binding mode was proposed. Namely, the hydrophobic cavity binds to fatty acid tails, while ‘X-R-R’ triad nearby the entrance of cavity recognizes the phosphate group head. Using molecular dynamics (MD) simulations, we further elaborated the mechanism of how the lysine-rich N-terminal domain assisting TIPE1 to favorably bind to phosphatidylinositol (PI). Beside small molecule substrate, we identified Gαi3 as a direct-binding partner of TIPE1 using GST pull-down assay and size-exclusion chromatography. Analyses of key-residue mutations and predicted complex structure revealed that the binding mode of TIPE1 to Gαi3 could be non-canonical. In summary, our findings narrowed down TIPE1’s position in Gαi3-related and PI-inducing signaling pathways.

Communicated by Ramaswamy H. Sarma

Keywords:

• TIPE1
• phosphatidylinositol
• lipid transfer protein
• tumor
• G-protein

Author contributions

S. C. prepared the protein samples of TIPE1 and potential partners, crystal screenings, and data collections in H. J.’s help. Y. Z. purified Gαi3 proteins and performed GST-pull down assays. X. H. performed molecular dynamic simulation. W.W. built the model and performed structural analysis. W.W., X. H. and Y. Z. prepared the figures and wrote the manuscript. W.W. supervised the project.

Acknowledgements

We thank the staff at the beamline 17U of the Shanghai Synchrotron Radiation Facility (Shanghai, People’s Republic of China) for technical assistance during data collection. We also thank all staff members of the Translational Medicine Core Facility of Advanced Medical Research Institute (AMRI), Shandong University. We are grateful to Xiaohong Liang and Chunhong Ma (Shandong University) for advice on revising the manuscript.

Data availability statement

The data that support this work is available from the corresponding authors upon reasonable request. The atomic model has been deposited to Protein Data Bank (PDB) under the accession code 8GYN.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by grants from National Natural Science Foundation of China (32171207, 31970584 and 82003590), and Shandong Provincial Natural Foundation (ZR2020YQ22). W.W. is also supported by a startup funding from Shandong University.