Structural basis of ligand recognition by PABC, a highly specific peptide-binding domain found in poly(A)-binding protein and a HECT ubiquitin ligase

EMBO J. 2004 Jan 28;23(2):272-81. doi: 10.1038/sj.emboj.7600048. Epub 2003 Dec 18.

Abstract

The C-terminal domain of poly(A)-binding protein (PABC) is a peptide-binding domain found in poly(A)-binding proteins (PABPs) and a HECT (homologous to E6-AP C-terminus) family E3 ubiquitin ligase. In protein synthesis, the PABC domain of PABP functions to recruit several translation factors possessing the PABP-interacting motif 2 (PAM2) to the mRNA poly(A) tail. We have determined the solution structure of the human PABC domain in complex with two peptides from PABP-interacting protein-1 (Paip1) and Paip2. The structures show a novel mode of peptide recognition, in which the peptide binds as a pair of beta-turns with extensive hydrophobic, electrostatic and aromatic stacking interactions. Mutagenesis of PABC and peptide residues was used to identify key protein-peptide interactions and quantified by isothermal calorimetry, surface plasmon resonance and GST pull-down assays. The results provide insight into the specificity of PABC in mediating PABP-protein interactions.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites
  • Carrier Proteins / chemistry
  • Carrier Proteins / metabolism
  • Conserved Sequence
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Peptide Initiation Factors / chemistry
  • Peptide Initiation Factors / metabolism
  • Peptides / chemistry
  • Peptides / metabolism
  • Poly(A)-Binding Proteins / chemistry*
  • Poly(A)-Binding Proteins / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • RNA-Binding Proteins
  • Repressor Proteins
  • Ribosomal Proteins / chemistry*
  • Static Electricity
  • Ubiquitin-Protein Ligases / chemistry*

Substances

  • Carrier Proteins
  • Ligands
  • PAIP1 protein, human
  • PAIP2 protein, human
  • Peptide Initiation Factors
  • Peptides
  • Poly(A)-Binding Proteins
  • RNA-Binding Proteins
  • Repressor Proteins
  • Ribosomal Proteins
  • UBR5 protein, human
  • Ubiquitin-Protein Ligases