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The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3

Nature Structural & Molecular Biology volume 11, pages 330–337 (2004)Cite this article

Abstract

Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast to human. We present a crystal structure at a resolution of 1.95 Å of the complex between the interacting domains of human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain). The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the β-sheet surface of the UPF3b RNP domain, which is generally used by these domains to bind nucleic acids. We show that the UPF3b RNP does not bind RNA, whereas the UPF2 construct and the complex do. Our results advance understanding of the molecular mechanisms underlying the NMD quality control process.

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Figure 1: Human UPF2 domain organization and sequence alignment of UPF2 and UPF3b.
Figure 2: Crystal structure of the complex between UPF2 and UPF3b.
Figure 3: Structure and surface characteristics of the UPF2–UPF3b complex and a comparison with the Y14–Mago complex.
Figure 4: Identification of critical interacting residues and RNA-binding activity of the UPF2–UPF3B complex.

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Acknowledgements

We thank members of EMBL-ESRF Joint Structural Biology Group, notably A. McCarthy and R. Ravelli, for assistance with data collection on ESRF beamlines and for help with the crystallographic analysis. We are grateful to C. Petosa and C. Mazza for their frequent advice throughout the project. We also thank L. Maquat (University of Rochester) for providing UPF2 and UPF3 cDNA.

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  1. European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP 181, Grenoble, F-38042 Cedex 9, France

    Jan Kadlec & Stephen Cusack

  2. European Molecular Biology Laboratory, Gene Expression Programme, Meyerhofstrasse 1, Heidelberg, 69117, Germany

    Elisa Izaurralde & Stephen Cusack

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Correspondence to Stephen Cusack.

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Kadlec, J., Izaurralde, E. & Cusack, S. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. Nat Struct Mol Biol 11, 330–337 (2004). https://doi.org/10.1038/nsmb741

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