Structural and biochemical studies of SLIP1-SLBP identify DBP5 and eIF3g as SLIP1-binding proteins

Nucleic Acids Res. 2013 Sep;41(16):7960-71. doi: 10.1093/nar/gkt558. Epub 2013 Jun 26.

Abstract

In metazoans, replication-dependent histone mRNAs end in a stem-loop structure instead of the poly(A) tail characteristic of all other mature mRNAs. This specialized 3' end is bound by stem-loop binding protein (SLBP), a protein that participates in the nuclear export and translation of histone mRNAs. The translational activity of SLBP is mediated by interaction with SLIP1, a middle domain of initiation factor 4G (MIF4G)-like protein that connects to translation initiation. We determined the 2.5 Å resolution crystal structure of zebrafish SLIP1 bound to the translation-activation domain of SLBP and identified the determinants of the recognition. We discovered a SLIP1-binding motif (SBM) in two additional proteins: the translation initiation factor eIF3g and the mRNA-export factor DBP5. We confirmed the binding of SLIP1 to DBP5 and eIF3g by pull-down assays and determined the 3.25 Å resolution structure of SLIP1 bound to the DBP5 SBM. The SBM-binding and homodimerization residues of SLIP1 are conserved in the MIF4G domain of CBP80/20-dependent translation initiation factor (CTIF). The results suggest how the SLIP1 homodimer or a SLIP1-CTIF heterodimer can function as platforms to bridge SLBP with SBM-containing proteins involved in different steps of mRNA metabolism.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • DEAD-box RNA Helicases / chemistry*
  • DEAD-box RNA Helicases / metabolism
  • Eukaryotic Initiation Factor-3 / chemistry
  • Eukaryotic Initiation Factor-3 / metabolism
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleocytoplasmic Transport Proteins / chemistry*
  • Nucleocytoplasmic Transport Proteins / metabolism
  • Protein Interaction Domains and Motifs
  • Protein Multimerization
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism
  • Sequence Alignment
  • Zebrafish Proteins / chemistry*
  • Zebrafish Proteins / metabolism

Substances

  • Eukaryotic Initiation Factor-3
  • Nucleocytoplasmic Transport Proteins
  • RNA-Binding Proteins
  • SLBP protein, zebrafish
  • Zebrafish Proteins
  • DDX19B protein, human
  • DEAD-box RNA Helicases

Associated data

  • PDB/4JHJ
  • PDB/4JHK