6KCZ

Solution structure of the ZnF-UBP domain of USP20/VDU2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional studies of USP20 ZnF-UBP domain by NMR.

Yang, Y.Ding, Y.Zhou, C.Wen, Y.Zhang, N.

(2019) Protein Sci 28: 1606-1619

  • DOI: 10.1002/pro.3675
  • Primary Citation of Related Structures:  
    6KCZ

  • PubMed Abstract: 
  • Deubiquitinase USP20/VDU2 has been demonstrated to play important roles in multiple cellular processes by controlling the life span of substrate proteins including hypoxia-inducible factor HIF1α, and so forth. USP20 contains four distinct structural domains including the N-terminal zinc-finger ubiquitin binding domain (ZnF-UBP), the catalytic domain (USP domain), and two tandem DUSP domains, and none of the structures for these four domains has been solved ...

    Deubiquitinase USP20/VDU2 has been demonstrated to play important roles in multiple cellular processes by controlling the life span of substrate proteins including hypoxia-inducible factor HIF1α, and so forth. USP20 contains four distinct structural domains including the N-terminal zinc-finger ubiquitin binding domain (ZnF-UBP), the catalytic domain (USP domain), and two tandem DUSP domains, and none of the structures for these four domains has been solved. Meanwhile, except for the ZnF-UBP domain, the biological functions for USP20's catalytic domain and tandem DUSP domains have been at least partially clarified. Here in this study, we determined the solution structure of USP20 ZnF-UBP domain and investigated its binding properties with mono-ubiquitin and poly-ubiquitin (K48-linked di-ubiquitin) by using NMR and molecular modeling techniques. USP20's ZnF-UBP domain forms a spherically shaped fold consisting of a central β-sheet with either one α-helix or two α-helices packed on each side of the sheet. However, although having formed a canonical core structure essential for ubiquitin recognition, USP20 ZnF-UBP presents weak ubiquitin binding capacity. The structural basis for understanding USP20 ZnF-UBP's ubiquitin binding capacity was revealed by NMR data-driven docking. Although the electrostatic interactions between D264 of USP5 (E87 in USP20 ZnF-UBP) and R74 of ubiquitin are kept, the loss of the extensive interactions formed between ubiquitin's di-glycine motif and the conserved and non-conserved residues of USP20 ZnF-UBP domain (W41, E55, and Y84) causes a significant decrease in its binding affinity to ubiquitin. Our findings indicate that USP20 ZnF-UBP domain might have a physiological role unrelated to its ubiquitin binding capacity.


    Organizational Affiliation

    University of the Chinese Academy of Sciences, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 20A99Homo sapiensMutation(s): 0 
Gene Names: USP20KIAA1003LSFR3AVDU2
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2K6 (Homo sapiens)
Explore Q9Y2K6 
Go to UniProtKB:  Q9Y2K6
PHAROS:  Q9Y2K6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 6KCZ Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Advisory, Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references