Journal Article

Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4

Sato, Yusuke, Tsuchiya, Hikaru, Okatsu, Kei, Tanaka, Keiji, Fukai, Shuya, Yamagata, Atsushi, Saeki, Yasushi

2019

Overview

Npl4 is likely to be the most upstream factor recognizing Lys48-linked polyubiquitylated substrates in the proteasomal degradation pathway in yeast. Along with Ufd1, Npl4 forms a heterodimer (UN), and functions as a cofactor for the Cdc48 ATPase. Here, we report the crystal structures of yeast Npl4 in complex with Lys48-linked diubiquitin and with the Npl4-binding motif of Ufd1. The distal and proximal ubiquitin moieties of Lys48-linked diubiquitin primarily interact with the C-terminal helix and N-terminal loop of the Npl4 C-terminal domain (CTD), respectively. Mutational analysis suggests that the CTD contributes to linkage selectivity and initial binding of ubiquitin chains. Ufd1 occupies a hydrophobic groove of the Mpr1/Pad1 N-terminal (MPN) domain of Npl4, which corresponds to the catalytic groove of the MPN domain of JAB1/MPN/Mov34 metalloenzyme (JAMM)-family deubiquitylating enzyme. This study provides important structural insights into the polyubiquitin chain recognition by the Cdc48–UN complex and its assembly. The Lys48-linked polyubiquitin-mediated proteasomal degradation in yeast depends on Cdc48 and its cofactors Ufd1 and Npl4. Here, the authors present crystal structures of Npl4 bound to Lys48-linked diubiquitin and the Npl4-binding motif of Ufd1, providing insights into the reaction mechanism of the Cdc48- Ufd1/Npl4 complex.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 13/1 / 631/337/474/2085 / 631/45/612/645 / 631/535/1266 / 82/103 / Biodegradation / Cofactors / Crystal structure / Crystallography, X-Ray / Crystals / Humanities and Social Sciences / multidisciplinary / Nucleocytoplasmic Transport Proteins - isolation & purification / Nucleocytoplasmic Transport Proteins - metabolism / Nucleocytoplasmic Transport Proteins - ultrastructure / Proteasome Endopeptidase Complex - metabolism / Proteasomes / Protein Binding / Protein Interaction Domains and Motifs / Reaction mechanisms / Recombinant Proteins - isolation & purification / Recombinant Proteins - metabolism / Recombinant Proteins - ultrastructure / Saccharomyces cerevisiae Proteins - isolation & purification / Saccharomyces cerevisiae Proteins - metabolism / Saccharomyces cerevisiae Proteins - ultrastructure / Science / Science (multidisciplinary) / Ubiquitin / Ubiquitin - metabolism / Ubiquitin - ultrastructure / Ubiquitination / Valosin Containing Protein - metabolism / Vesicular Transport Proteins - isolation & purification / Vesicular Transport Proteins - metabolism / Vesicular Transport Proteins - ultrastructure / Yeast