5TXK

CRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Expansion of DUB functionality generated by alternative isoforms - USP35, a case study.

Leznicki, P.Natarajan, J.Bader, G.Spevak, W.Schlattl, A.Abdul Rehman, S.A.Pathak, D.Weidlich, S.Zoephel, A.Bordone, M.C.Barbosa-Morais, N.L.Boehmelt, G.Kulathu, Y.

(2018) J. Cell. Sci. 131: --

  • DOI: 10.1242/jcs.212753

  • PubMed Abstract: 
  • Protein ubiquitylation is a dynamic post-translational modification that can be reversed by deubiquitylating enzymes (DUBs). It is unclear how the small number (∼100) of DUBs present in mammalian cells regulate the thousands of different ubiquitylati ...

    Protein ubiquitylation is a dynamic post-translational modification that can be reversed by deubiquitylating enzymes (DUBs). It is unclear how the small number (∼100) of DUBs present in mammalian cells regulate the thousands of different ubiquitylation events. Here, we analysed annotated transcripts of human DUBs and found ∼300 ribosome-associated transcripts annotated as protein coding, which thus increases the total number of DUBs. By using USP35, a poorly studied DUB, as a case study, we provide evidence that alternative isoforms contribute to the functional expansion of DUBs. We show that there are two different USP35 isoforms that localise to different intracellular compartments and have distinct functions. Our results reveal that isoform 1 is an anti-apoptotic factor that inhibits staurosporine- and TNF-related apoptosis-inducing ligand (TRAIL; also known as TNFSF10)-induced apoptosis. In contrast, USP35 isoform 2 is an integral membrane protein of the endoplasmic reticulum (ER) that is also present at lipid droplets. Manipulations of isoform 2 levels cause rapid ER stress, likely through deregulation of lipid homeostasis, and lead to cell death. Our work highlights how alternative isoforms provide functional expansion of DUBs and sets directions for future research.This article has an associated First Person interview with the first author of the paper.


    Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer Gasse 5-11, 1120 Vienna, Austria.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK pawel.leznicki@manchester.ac.uk ykulathu@dundee.ac.uk.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 35,Ubiquitin carboxyl-terminal hydrolase 35
A
372Homo sapiensMutation(s): 1 
Gene Names: USP35 (KIAA1372, USP34)
EC: 3.4.19.12
Find proteins for Q9P2H5 (Homo sapiens)
Go to Gene View: USP35
Go to UniProtKB:  Q9P2H5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.235α = 90.00
b = 104.235β = 90.00
c = 106.381γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata reduction
BUSTER-TNTrefinement
AutoPROCdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references
  • Version 1.2: 2019-10-16
    Type: Data collection