Recognition of the Diglycine C-End Degron by CRL2 KLHDC2 Ubiquitin Ligase

Mol Cell. 2018 Dec 6;72(5):813-822.e4. doi: 10.1016/j.molcel.2018.10.021.

Abstract

Aberrant proteins can be deleterious to cells and are cleared by the ubiquitin-proteasome system. A group of C-end degrons that are recognized by specific cullin-RING ubiquitin E3 ligases (CRLs) has recently been identified in some of these abnormal polypeptides. Here, we report three crystal structures of a CRL2 substrate receptor, KLHDC2, in complex with the diglycine-ending C-end degrons of two early-terminated selenoproteins and the N-terminal proteolytic fragment of USP1. The E3 recognizes the degron peptides in a similarly coiled conformation and cradles their C-terminal diglycine with a deep surface pocket. By hydrogen bonding with multiple backbone carbonyls of the peptides, KLHDC2 further locks in the otherwise degenerate degrons with a compact interface and unexpected high affinities. Our results reveal the structural mechanism by which KLHDC2 recognizes the simplest C-end degron and suggest a functional necessity of the E3 to tightly maintain the low abundance of its select substrates.

Keywords: C-end degron; DesCEND; E3; KLHDC2; USP1; crystal structure; cullin; protein degradation; selenoproteins; ubiquitin.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Antigens, Neoplasm / chemistry*
  • Antigens, Neoplasm / genetics
  • Antigens, Neoplasm / metabolism
  • Baculoviridae / genetics
  • Baculoviridae / metabolism
  • Binding Sites
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • Glycylglycine / chemistry*
  • Glycylglycine / metabolism
  • HEK293 Cells
  • Humans
  • Kinetics
  • Molecular Docking Simulation
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Selenoproteins / chemistry*
  • Selenoproteins / genetics
  • Selenoproteins / metabolism
  • Spodoptera
  • Substrate Specificity
  • Ubiquitin-Specific Proteases / chemistry*
  • Ubiquitin-Specific Proteases / genetics
  • Ubiquitin-Specific Proteases / metabolism

Substances

  • Antigens, Neoplasm
  • KLHDC2 protein, human
  • Recombinant Proteins
  • Selenoproteins
  • selenoprotein K, human
  • Glycylglycine
  • USP1 protein, human
  • Ubiquitin-Specific Proteases
  • Proteasome Endopeptidase Complex