Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome

Simone Cavadini; Eric S Fischer; Richard D Bunker; Alessandro Potenza; Gondichatnahalli M Lingaraju; Kenneth N Goldie; Weaam I Mohamed; Mahamadou Faty; Georg Petzold; Rohan E J Beckwith; Ritesh B Tichkule; Ulrich Hassiepen; Wassim Abdulrahman; Radosav S Pantelic; Syota Matsumoto; Kaoru Sugasawa; Henning Stahlberg; Nicolas H Thomä

doi:10.1038/nature17416

Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome

Nature. 2016 Mar 31;531(7596):598-603. doi: 10.1038/nature17416.

Authors

Simone Cavadini^{1

2}, Eric S Fischer^{1

2

3

4}, Richard D Bunker^{1

2}, Alessandro Potenza^{1

2}, Gondichatnahalli M Lingaraju^{1

2}, Kenneth N Goldie⁵, Weaam I Mohamed^{1

2}, Mahamadou Faty^{1

2}, Georg Petzold^{1

2}, Rohan E J Beckwith⁶, Ritesh B Tichkule⁶, Ulrich Hassiepen⁷, Wassim Abdulrahman^{1

2}, Radosav S Pantelic^{5

8}, Syota Matsumoto^{9

10}, Kaoru Sugasawa^{9

10}, Henning Stahlberg⁵, Nicolas H Thomä^{1

2}

Affiliations

¹ Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
² University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
³ Department of Cancer Biology, Dana-Farber Cancer Institute, LC-4312, 360 Longwood Avenue, Boston, Massachusetts 02215, USA.
⁴ Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, USA.
⁵ Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, 4058 Basel, Switzerland.
⁶ Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
⁷ Novartis Pharma AG, Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland.
⁸ Gatan R&D, 5974 W. Las Positas Boulevard, Pleasanton, California 94588, USA.
⁹ Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan.
¹⁰ Graduate School of Science, Kobe University, Kobe, 657-8501, Japan.

PMID: 27029275
DOI: 10.1038/nature17416

Abstract

The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A-RBX1-DDB1-DDB2 complex (CRL4A(DDB2)) monitors the genome for ultraviolet-light-induced DNA damage. CRL4A(DBB2) is inactive in the absence of damaged DNA and requires CSN to regulate the repair process. The structural basis of CSN binding to CRL4A(DDB2) and the principles of CSN activation are poorly understood. Here we present cryo-electron microscopy structures for CSN in complex with neddylated CRL4A ligases to 6.4 Å resolution. The CSN conformers defined by cryo-electron microscopy and a novel apo-CSN crystal structure indicate an induced-fit mechanism that drives CSN activation by neddylated CRLs. We find that CSN and a substrate cannot bind simultaneously to CRL4A, favouring a deneddylated, inactive state for substrate-free CRL4 complexes. These architectural and regulatory principles appear conserved across CRL families, allowing global regulation by CSN.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Allosteric Regulation
Apoproteins / chemistry
Apoproteins / metabolism
Apoproteins / ultrastructure
Binding Sites
Biocatalysis*
COP9 Signalosome Complex
Carrier Proteins / chemistry
Carrier Proteins / metabolism
Carrier Proteins / ultrastructure
Cryoelectron Microscopy
Crystallography, X-Ray
Cullin Proteins / chemistry
Cullin Proteins / metabolism
Cullin Proteins / ultrastructure
DNA Damage
DNA-Binding Proteins / chemistry
DNA-Binding Proteins / metabolism
DNA-Binding Proteins / ultrastructure
Humans
Kinetics
Models, Molecular
Multiprotein Complexes / chemistry
Multiprotein Complexes / metabolism*
Multiprotein Complexes / ultrastructure*
Peptide Hydrolases / chemistry
Peptide Hydrolases / metabolism*
Peptide Hydrolases / ultrastructure*
Protein Binding
Ubiquitination
Ubiquitins / metabolism

Substances

Apoproteins
CUL4A protein, human
Carrier Proteins
Cullin Proteins
DDB1 protein, human
DDB2 protein, human
DNA-Binding Proteins
Multiprotein Complexes
RBX1 protein, human
Ubiquitins
Peptide Hydrolases
COP9 Signalosome Complex

Associated data

PDB/4WSN