Crystal structure of deubiquitinase MINDY-1

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

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MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes.

Abdul Rehman, S.A.Kristariyanto, Y.A.Choi, S.Y.Nkosi, P.J.Weidlich, S.Labib, K.Hofmann, K.Kulathu, Y.

(2016) Mol Cell 63: 146-155

  • DOI: https://doi.org/10.1016/j.molcel.2016.05.009
  • Primary Citation of Related Structures:  
    5JKN, 5JQS

  • PubMed Abstract: 

    Deubiquitinating enzymes (DUBs) remove ubiquitin (Ub) from Ub-conjugated substrates to regulate the functional outcome of ubiquitylation. Here we report the discovery of a new family of DUBs, which we have named MINDY (motif interacting with Ub-containing novel DUB family). Found in all eukaryotes, MINDY-family DUBs are highly selective at cleaving K48-linked polyUb, a signal that targets proteins for degradation. We identify the catalytic activity to be encoded within a previously unannotated domain, the crystal structure of which reveals a distinct protein fold with no homology to any of the known DUBs. The crystal structure of MINDY-1 (also known as FAM63A) in complex with propargylated Ub reveals conformational changes that realign the active site for catalysis. MINDY-1 prefers cleaving long polyUb chains and works by trimming chains from the distal end. Collectively, our results reveal a new family of DUBs that may have specialized roles in regulating proteostasis.

  • Organizational Affiliation

    Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Cologne, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM63A289Homo sapiensMutation(s): 0 
Gene Names: FAM63AKIAA1390MINDY1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5J2 (Homo sapiens)
Explore Q8N5J2 
Go to UniProtKB:  Q8N5J2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N5J2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.671α = 90
b = 99.671β = 90
c = 165.123γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection