5JKN

Crystal structure of deubiquitinase MINDY-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.molcel.2016.05.009
  • Primary Citation of Related Structures:  

  • 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-conta ...

    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.,MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.,MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: ykulathu@dundee.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein FAM63A
A
289Homo sapiensMutation(s): 0 
Gene Names: MINDY1 (FAM63A, KIAA1390)
EC: 3.4.19.12
Find proteins for Q8N5J2 (Homo sapiens)
Go to Gene View: MINDY1
Go to UniProtKB:  Q8N5J2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.671α = 90.00
b = 99.671β = 90.00
c = 165.123γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-06-29
    Type: Database references
  • Version 1.2: 2016-07-20
    Type: Database references