6OB1

Structure of WHB in complex with Ubiquitin Variant


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site.

Watson, E.R.Grace, C.R.R.Zhang, W.Miller, D.J.Davidson, I.F.Prabu, J.R.Yu, S.Bolhuis, D.L.Kulko, E.T.Vollrath, R.Haselbach, D.Stark, H.Peters, J.M.Brown, N.G.Sidhu, S.S.Schulman, B.A.

(2019) Proc.Natl.Acad.Sci.USA 116: 17280-17289

  • DOI: 10.1073/pnas.1902889116

  • PubMed Abstract: 
  • Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E ...

    Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at "exosites." However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.


    Organizational Affiliation

    Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S3E1.,Medical University of Vienna, 1090 Vienna, Austria.,Research Institute of Molecular Pathology, Vienna BioCenter, 1030 Vienna, Austria.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S3E1.,Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S3E1; sachdev.sidhu@utoronto.ca schulman@biochem.mpg.de.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105; sachdev.sidhu@utoronto.ca schulman@biochem.mpg.de.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
75N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
75N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Anaphase-promoting complex subunit 2
C
90Homo sapiensMutation(s): 0 
Gene Names: ANAPC2 (APC2, KIAA1406)
Find proteins for Q9UJX6 (Homo sapiens)
Go to Gene View: ANAPC2
Go to UniProtKB:  Q9UJX6
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR35GM128855
National Institutes of Health/National Human Genome Research InstituteUnited StatesR37GM065930

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-09-04
    Type: Data collection, Database references