5WCH

Crystal structure of the catalytic domain of human USP9X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X.

Paudel, P.Zhang, Q.Leung, C.Greenberg, H.C.Guo, Y.Chern, Y.H.Dong, A.Li, Y.Vedadi, M.Zhuang, Z.Tong, Y.

(2019) Proc Natl Acad Sci U S A 116: 7288-7297

  • DOI: 10.1073/pnas.1815027116
  • Primary Citation of Related Structures:  
    5WCH

  • PubMed Abstract: 
  • USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulation of USP9X has been linked to cancers and X-linked intellectual disability. Here, we report the crystal structure of the USP9X catalytic domain at 2.5-Å ...

    USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulation of USP9X has been linked to cancers and X-linked intellectual disability. Here, we report the crystal structure of the USP9X catalytic domain at 2.5-Å resolution. The structure reveals a canonical USP-fold comprised of fingers, palm, and thumb subdomains, as well as an unusual β-hairpin insertion. The catalytic triad of USP9X is aligned in an active configuration. USP9X is exclusively active against ubiquitin (Ub) but not Ub-like modifiers. Cleavage assays with di-, tri-, and tetraUb chains show that the USP9X catalytic domain has a clear preference for K11-, followed by K63-, K48-, and K6-linked polyUb chains. Using a set of activity-based diUb and triUb probes (ABPs), we demonstrate that the USP9X catalytic domain has an exo-cleavage preference for K48- and endo-cleavage preference for K11-linked polyUb chains. The structure model and biochemical data suggest that the USP9X catalytic domain harbors three Ub binding sites, and a zinc finger in the fingers subdomain and the β-hairpin insertion both play important roles in polyUb chain processing and linkage specificity. Furthermore, unexpected labeling of a secondary, noncatalytic cysteine located on a blocking loop adjacent to the catalytic site by K11-diUb ABP implicates a previously unreported mechanism of polyUb chain recognition. The structural features of USP9X revealed in our study are critical for understanding its DUB activity. The new Ub-based ABPs form a set of valuable tools to understand polyUb chain processing by the cysteine protease class of DUBs.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ubiquitin carboxyl-terminal hydrolase FAF-XABCD421Homo sapiensMutation(s): 2 
Gene Names: USP9XDFFRXFAMUSP9
EC: 3.4.19.12
Find proteins for Q93008 (Homo sapiens)
Explore Q93008 
Go to UniProtKB:  Q93008
NIH Common Fund Data Resources
PHAROS  Q93008
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
C
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.372α = 90
b = 79.048β = 103.76
c = 131.933γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.3: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.4: 2019-04-24
    Changes: Data collection, Database references