7W3U

USP34 catalytic domain in complex with UbPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural Insights into the Catalytic Mechanism and Ubiquitin Recognition of USP34.

Xu, G.Su, H.Lu, L.Liu, X.Zhao, L.Tang, B.Ming, Z.

(2022) J Mol Biol 434: 167634-167634

  • DOI: https://doi.org/10.1016/j.jmb.2022.167634
  • Primary Citation of Related Structures:  
    7W3R, 7W3U

  • PubMed Abstract: 

    Ubiquitination, an important posttranslational modification, participates in virtually all aspects of cellular functions and is reversed by deubiquitinating enzymes (DUBs). Ubiquitin-specific protease 34 (USP34) plays an essential role in cancer, neurodegenerative diseases, and osteogenesis. Despite its functional importance, how USP34 recognizes ubiquitin and catalyzes deubiquitination remains structurally uncharacterized. Here, we report the crystal structures of the USP34 catalytic domain in free state and after binding with ubiquitin. In the free state, USP34 adopts an inactive conformation, which contains a misaligned catalytic histidine in the triad. Comparison of USP34 structures before and after ubiquitin binding reveals a structural basis for ubiquitin recognition and elucidates a mechanism by which the catalytic triad is realigned. Transition from an open inactive state to a relatively closed active state is coupled to a process by which the "fingertips" of USP34 intimately grip ubiquitin, and this has not been reported before. Our structural and biochemical analyses provide important insights into the catalytic mechanism and ubiquitin recognition of USP34.


  • Organizational Affiliation

    State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 34
A, B, C
384Homo sapiensMutation(s): 0 
Gene Names: USP34KIAA0570KIAA0729
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q70CQ2 (Homo sapiens)
Explore Q70CQ2 
Go to UniProtKB:  Q70CQ2
PHAROS:  Q70CQ2
GTEx:  ENSG00000115464 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70CQ2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-B
D, E, F
75Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.02α = 90
b = 71.33β = 90
c = 111.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)31700052
National Natural Science Foundation of China (NSFC)81871938

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 2.0: 2024-02-07
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-04-24
    Changes: Advisory, Derived calculations