Structural and mechanistic insights into the arginine/lysine-rich peptide motifs that interact with P97/VCP

Biochim Biophys Acta. 2013 Dec;1834(12):2672-8. doi: 10.1016/j.bbapap.2013.09.021. Epub 2013 Oct 4.

Abstract

P97 protein, also referred to as valosin-containing protein (VCP), is an AAA-ATPase (ATPase associated with a variety of cellular activities) that mediates vital cellular activities with the cooperation of many cofactors. A group of cofactors interact with the N-terminal domain of P97 (P97N) through their Arg/Lys-rich peptide motifs. We investigated the interactions between P97 and these motifs, including VCP-binding motif (VBM) and VCP-interacting motif (VIM). The solution structures of the VBM motif from HRD1 and the VIM motif from SVIP are both comprised mainly of a single α-helix. The VIM motifs generally have stronger P97N-binding affinities than the VBMs, and SVIP (VIM) can compete with HRD1-VBM for the interaction, providing a possibility that VIM-containing proteins (such as SVIP) act as competitors against VBM-containing proteins (such as HRD1) for interacting with P97. Based on biochemical features of the VBM motifs, we also identified NUB1L (NEDD8 ultimate buster-1 long) as a novel VBM-containing protein, which is involved in proteasomal degradation of NEDD8 through the P97 pathway.

Keywords: AAA; ATPase associated with a variety of cellular activities; Arginine/lysine-rich; BS1; ERAD; ITC; Interaction; NMR; P97-ND1; P97/VCP; P97N; Structure; VBM; VCP; VCP-binding motif; VCP-interacting motif; VIM; binding site 1; endoplasmic reticulum-associated degradation; isothermal titration calorimetry; nuclear magnetic resonance; the N and D1 domains of P97 (residues 1–458); the N-terminal domain of P97 (residues 1–213); valosin-containing protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing
  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism*
  • Amino Acid Motifs
  • Arginine / chemistry
  • Arginine / genetics
  • Arginine / metabolism
  • Carrier Proteins / chemistry
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism*
  • Cell Cycle Proteins / chemistry
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism*
  • HEK293 Cells
  • Humans
  • Membrane Proteins / chemistry
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism*
  • NEDD8 Protein
  • Peptides / chemistry
  • Peptides / genetics
  • Peptides / metabolism*
  • Phosphate-Binding Proteins
  • Proline / chemistry
  • Proline / genetics
  • Proline / metabolism
  • Proteasome Endopeptidase Complex / chemistry
  • Proteasome Endopeptidase Complex / genetics
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Binding
  • Proteolysis
  • Transcription Factors / chemistry
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Ubiquitin-Protein Ligases / chemistry
  • Ubiquitin-Protein Ligases / genetics
  • Ubiquitin-Protein Ligases / metabolism*
  • Ubiquitins / chemistry
  • Ubiquitins / genetics
  • Ubiquitins / metabolism
  • Valosin Containing Protein

Substances

  • Adaptor Proteins, Signal Transducing
  • Carrier Proteins
  • Cell Cycle Proteins
  • Membrane Proteins
  • NEDD8 Protein
  • NEDD8 protein, human
  • NUB1 protein, human
  • Peptides
  • Phosphate-Binding Proteins
  • SVIP protein, human
  • Transcription Factors
  • Ubiquitins
  • Arginine
  • Proline
  • SYVN1 protein, human
  • Ubiquitin-Protein Ligases
  • Proteasome Endopeptidase Complex
  • Adenosine Triphosphatases
  • VCP protein, human
  • Valosin Containing Protein