Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking

Ameerul, Aalam; Almasmoum, Hibah; Pavanello, Lorenzo; Dominguez, Cyril; Winkler, Gerlof Sebastiaan

Abstract

Degradation of cytoplasmic mRNA in eukaryotes involves the shortening and removal of the mRNA poly(A) tail by poly(A)-selective ribonuclease (deadenylase) enzymes. In human cells, BTG2 can stimulate deadenylation of poly(A) bound by cytoplasmic poly(A)-binding protein PABPC1. This involves the concurrent binding by BTG2 of PABPC1 and the Caf1/CNOT7 nuclease subunit of the Ccr4-Not deadenylase complex. To understand in molecular detail how PABPC1 and BTG2 interact, we set out to identify amino acid residues of PABPC1 and BTG2 contributing to the interaction. To this end, we first used algorithms to predict PABPC1 interaction surfaces. Comparison of the predicted interaction surface with known residues involved in the binding to poly(A) resulted in the identification of a putative interaction surface for BTG2. Subsequently, we used pulldown assays to confirm the requirement of PABPC1 residues for the interaction with BTG2. Analysis of RNA-binding by PABPC1 variants indicated that PABPC1 residues required for interaction with BTG2 do not interfere with poly(A) binding. After further defining residues of BTG2 that are required for the interaction with PABPC1, we used information from published NMR chemical shift perturbation experiments to guide docking and generate a structural model of the BTG2-PABPC1 complex. A quaternary poly(A)-PABPC1-BTG2-Caf1/CNOT7 model showed that the 3′ end of poly(A) RNA is directed towards the catalytic centre of Caf1/CNOT7, thereby providing a rationale for enhanced deadenylation by Caf1/CNOT7 in the presence of BTG2 and PABPC1.

Citation

Ameerul, A., Almasmoum, H., Pavanello, L., Dominguez, C., & Winkler, G. S. (2022). Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking. Journal of Molecular Biology, 434(14), Article 167662. https://doi.org/10.1016/j.jmb.2022.167662

• Journal Article Type: Article
• Acceptance Date: May 24, 2022
• Online Publication Date: Jun 10, 2022
• Publication Date: Jul 30, 2022
• Deposit Date: May 27, 2022
• Publicly Available Date: Jun 11, 2023
• Journal: Journal of Molecular Biology
• Print ISSN: 0022-2836
• Electronic ISSN: 1089-8638
• Publisher: Elsevier BV
• Peer Reviewed: Peer Reviewed
• Volume: 434
• Issue: 14
• Article Number: 167662
• DOI: https://doi.org/10.1016/j.jmb.2022.167662
• Keywords: Molecular Biology; Structural Biology
• Public URL: https://nottingham-repository.worktribe.com/output/8225158
• Publisher URL: https://www.sciencedirect.com/science/article/pii/S0022283622002546?via%3Dihub