Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41083.89 
• Atom Count: 3104 
• Residue Count: 365 
• Unique protein chains: 2

5JQS

Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin

• DOI: 10.2210/pdb5JQS/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus, Homo sapiens
• Expression System: Bos taurus, Escherichia coli


• Deposited: 2016-05-05 Released: 2016-06-22 
• Deposition Author(s): Abdul Rehman, S.A., Kulathu, Y.

---

Experimental Data Snapshot

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

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

• PubMed: 27292798 
• DOI: 10.1016/j.molcel.2016.05.009
• Primary Citation of Related Structures:  
  5JKN


• 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: 

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
Molecule	Chains	Sequence Length	Organism	Details
Protein FAM63A	A	289	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-40S ribosomal protein S27a	D	76	Bos taurus	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
AYE	A	prop-2-en-1-amine ALLYLAMINE C3 H7 N VVJKKWFAADXIJK-UHFFFAOYSA-N
DIO	A	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

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 = 82.336	α = 90.00
b = 82.336	β = 90.00
c = 332.464	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-05 
• Released Date: 2016-06-22 
• Deposition Author(s): Abdul Rehman, S.A., Kulathu, Y.

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