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

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 Cterminus) 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 b-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 pulldown assays. The results provide insight into the specificity of PABC in mediating PABP-protein interactions.

Makorin Ring Zinc Finger Protein 1 (MKRN1), a Novel Poly(A)-binding Protein-interacting Protein, Stimulates Translation in Nerve Cells

“…A closer inspection (Fig. 3A) revealed that the sequence spanning amino acids 161-176 is very similar to PAM2 motifs within PAIP1 and -2 and Ataxin-2 (ATXN2), respectively (46). Yet in MKRN1-short a highly conserved leucine (Leu 128 in PAIP1, Leu 111 in PAIP2, and Leu 913 in ATXN2) is replaced by aspartate (Asp 165 ).…”

Phosphorylation at intrinsically disordered regions of PAM2 motif-containing proteins modulates their interactions with PABPC1 and influences mRNA fate

“…Structural data show that the PAM2 motif binds to the highly conserved MLLE domain in the C-terminal region of PABPC1 (Kozlov et al 2004;Jinek et al 2010;Kozlov and Gehring 2010). Among the PAM2-containing proteins are several well-studied translation and mRNA decay factors, including PAIP1 (Roy et al 2002), PAIP2 (Khaleghpour et al 2001), Tnrc6 (Eystathioy et al 2003), translation termination factor 3 (eRF3) (Hoshino et al 1999), PABP-dependent poly(A) nuclease subunit 3 (Pan3) (Uchida et al 2004), and transducer of erbB-2 proteins (Tob) (Ikematsu et al 1999).…”

Functional Roles of the E3 Ubiquitin Ligase UBR5 in Cancer

“…The MLLE/PABC domain is thought to be a protein-protein interaction motif (e.g., known to bind substrates such as PAIP2; refs. 31,32) and may regulate ubiquitin transfer catalyzed by the HECT domain (33).…”