Recognition of the Diglycine C-End Degron by CRL2KLHDC2 Ubiquitin Ligase

Domniţa-Valeria Rusnac; Hsiu-Chuan Lin; Daniele Canzani; Karena X Tien; Thomas R Hinds; Ashley F Tsue; Matthew F Bush; Hsueh-Chi S Yen; Ning Zheng

doi:10.1016/j.molcel.2018.10.021

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.

Authors

Domniţa-Valeria Rusnac¹, Hsiu-Chuan Lin², Daniele Canzani³, Karena X Tien¹, Thomas R Hinds¹, Ashley F Tsue¹, Matthew F Bush³, Hsueh-Chi S Yen², Ning Zheng⁴

Affiliations

¹ Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
² Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.
³ Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
⁴ Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA. Electronic address: nzheng@uw.edu.

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.

Published by Elsevier Inc.

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

Abstract

Publication types

MeSH terms

Substances

Grants and funding