5LG7

Solution NMR structure of Tryptophan to Arginine mutant of Arkadia RING domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 31 
  • Conformers Submitted: 31 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Residue Specific Insight into the Arkadia E3 Ubiquitin Ligase Activity and Conformational Plasticity.

Birkou, M.Chasapis, C.T.Marousis, K.D.Loutsidou, A.K.Bentrop, D.Lelli, M.Herrmann, T.Carthy, J.M.Episkopou, V.Spyroulias, G.A.

(2017) J. Mol. Biol. 429: 2373-2386

  • DOI: 10.1016/j.jmb.2017.06.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Arkadia (Rnf111) is an E3 ubiquitin ligase that plays a central role in the amplification of transforming growth factor beta (TGF-β) signaling responses by targeting for degradation the negative regulators of the pathway, Smad6 and Smad7, and the nuc ...

    Arkadia (Rnf111) is an E3 ubiquitin ligase that plays a central role in the amplification of transforming growth factor beta (TGF-β) signaling responses by targeting for degradation the negative regulators of the pathway, Smad6 and Smad7, and the nuclear co-repressors Ski and Skil (SnoN). Arkadia's function in vivo depends on the really interesting new gene (RING)-H2 interaction with the E2 enzyme UbcH5b in order to ligate ubiquitin chains on its substrates. A conserved tryptophan (W972) in the C-terminal α-helix is widely accepted as essential for E2 recruitment and interaction and thus also for E3 enzymatic activity. The present NMR-driven study provides an atomic-level investigation of the structural and dynamical properties of two W972 Arkadia RING mutants, attempting to illuminate for the first time the differences between a functional and a nonfunctional mutant W972A and W972R, respectively. A TGF-β-responsive promoter driving luciferase was used to assay for Arkadia function in vivo. These experiments showed that the Arkadia W972A mutant has the same activity as wild-type (WT) Arkadia in enhancing TGF-β signaling responses, while W972R does not. Only minor structural differences exist between the W972A RING domain and WT-RING. In contrast, the W972R mutant hardly interacts with E2. The loss of function correlates with structural changes in the C-terminal α-helix and an increase in the distance between the Zn(II) ions. Our data show that the position occupied by W972 within WT Arkadia is critical for the function of RING and that it depends on the nature of the residue at this position.


    Organizational Affiliation

    Department of Pharmacy, University of Patras, GR-26504 Patras, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Arkadia
A
69Homo sapiensMutation(s): 1 
Gene Names: RNF111
EC: 2.3.2.27
Find proteins for Q6ZNA4 (Homo sapiens)
Go to Gene View: RNF111
Go to UniProtKB:  Q6ZNA4
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 31 
  • Conformers Submitted: 31 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FP7-CAPACITIES - Research Potentials REGPOT "SEE-DRUG"Greece285950

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Database references
  • Version 1.3: 2019-05-08
    Type: Data collection