5JQS

Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 

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

    MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
D
76Bos taurusMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62992 (Bos taurus)
Go to Gene View: RPS27A
Go to UniProtKB:  P62992
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AYE
Query on AYE

Download SDF File 
Download CCD File 
A
prop-2-en-1-amine
ALLYLAMINE
C3 H7 N
VVJKKWFAADXIJK-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download SDF File 
Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.336α = 90.00
b = 82.336β = 90.00
c = 332.464γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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