Unusual bipartite mode of interaction between the nonsense-mediated decay factors, UPF1 and UPF2

EMBO J. 2009 Aug 5;28(15):2293-306. doi: 10.1038/emboj.2009.175. Epub 2009 Jun 25.

Abstract

Nonsense-mediated decay (NMD) is a eukaryotic quality control mechanism that degrades mRNAs carrying premature stop codons. In mammalian cells, NMD is triggered when UPF2 bound to UPF3 on a downstream exon junction complex interacts with UPF1 bound to a stalled ribosome. We report structural studies on the interaction between the C-terminal region of UPF2 and intact UPF1. Crystal structures, confirmed by EM and SAXS, show that the UPF1 CH-domain is docked onto its helicase domain in a fixed configuration. The C-terminal region of UPF2 is natively unfolded but binds through separated alpha-helical and beta-hairpin elements to the UPF1 CH-domain. The alpha-helical region binds sixfold more weakly than the beta-hairpin, whereas the combined elements bind 80-fold more tightly. Cellular assays show that NMD is severely affected by mutations disrupting the beta-hairpin binding, but not by those only affecting alpha-helix binding. We propose that the bipartite mode of UPF2 binding to UPF1 brings the ribosome and the EJC in close proximity by forming a tight complex after an initial weak encounter with either element.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Crystallography, X-Ray
  • DNA Mutational Analysis
  • Microscopy, Electron
  • Molecular Sequence Data
  • Mutation, Missense
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Interaction Mapping*
  • Protein Structure, Quaternary
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA Helicases
  • RNA Stability*
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins
  • Scattering, Small Angle
  • Sequence Alignment
  • Trans-Activators / chemistry
  • Trans-Activators / metabolism*
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism*

Substances

  • RNA, Messenger
  • RNA-Binding Proteins
  • Trans-Activators
  • Transcription Factors
  • UPF2 protein, human
  • RNA Helicases
  • UPF1 protein, human

Associated data

  • PDB/2WJV
  • PDB/2WJY