5H7S

Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of LNX1:Ubc13~Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1.

Nayak, D.Sivaraman, J.

(2018) J. Mol. Biol. 430: 1173-1188

  • DOI: 10.1016/j.jmb.2018.02.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LNX1 (ligand of numb protein-X1) is a RING and PDZ domain-containing E3 ubiquitin ligase that ubiquitinates human c-Src kinase. Here, we report the identification and structure of the ubiquitination domain of LNX1, the identification of Ubc13/Ube2V2 ...

    LNX1 (ligand of numb protein-X1) is a RING and PDZ domain-containing E3 ubiquitin ligase that ubiquitinates human c-Src kinase. Here, we report the identification and structure of the ubiquitination domain of LNX1, the identification of Ubc13/Ube2V2 as a functional E2 in vitro, and the structural and functional studies of the Ubc13~Ub intermediate in complex with the ubiquitination domain of LNX1. The RING domain of LNX1 is embedded between two zinc-finger motifs (Zn-RING-Zn), both of which are crucial for its ubiquitination activity. In the heterodimeric complex, the ubiquitin of one monomer shares more buried surface area with LNX1 of the other monomer and these interactions are unique and essential for catalysis. This study reveals how the LNX1 RING domain is structurally and mechanistically dependent on other motifs for its E3 ligase activity, and describes how dimeric LNX1 recruits ubiquitin-loaded Ubc13 for Ub transfer via E3 ligase-mediated catalysis.


    Organizational Affiliation

    Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543. Electronic address: dbsjayar@nus.edu.sg.,Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like 1
E, F
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase LNX
D, B
128Homo sapiensMutation(s): 0 
Gene Names: LNX1 (LNX, PDZRN2)
EC: 2.3.2.27
Find proteins for Q8TBB1 (Homo sapiens)
Go to Gene View: LNX1
Go to UniProtKB:  Q8TBB1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
A, C
152Homo sapiensMutation(s): 2 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.241 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.372α = 90.00
b = 122.372β = 90.00
c = 135.199γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)SingaporeR154000625112

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references