5DKA

A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNF125


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.

Bijlmakers, M.J.Teixeira, J.M.Boer, R.Mayzel, M.Puig-Sarries, P.Karlsson, G.Coll, M.Pons, M.Crosas, B.

(2016) Sci Rep 6: 29232-29232

  • DOI: 10.1038/srep29232

  • PubMed Abstract: 
  • The activity of RING ubiquitin ligases (E3s) depends on an interaction between the RING domain and ubiquitin conjugating enzymes (E2), but posttranslational events or additional structural elements, yet largely undefined, are frequently required to e ...

    The activity of RING ubiquitin ligases (E3s) depends on an interaction between the RING domain and ubiquitin conjugating enzymes (E2), but posttranslational events or additional structural elements, yet largely undefined, are frequently required to enhance or regulate activity. Here, we show for the ubiquitin ligase RNF125 that, in addition to the RING domain, a C2HC Zn finger (ZnF) is crucial for activity, and a short linker sequence (Li2(120-128)) enhances activity. The contribution of these regions was first shown with truncated proteins, and the essential role of the ZnF was confirmed with mutations at the Zn chelating Cys residues. Using NMR, we established that the C2HC ZnF/Li2(120-128) region is crucial for binding of the RING domain to the E2 UbcH5a. The partial X-ray structure of RNF125 revealed the presence of extensive intramolecular interactions between the RING and C2HC ZnF. A mutation at one of the contact residues in the C2HC ZnF, a highly conserved M112, resulted in the loss of ubiquitin ligase activity. Thus, we identified the structural basis for an essential role of the C2HC ZnF and conclude that this domain stabilizes the RING domain, and is therefore required for binding of RNF125 to an E2.


    Organizational Affiliation

    Swedish NMR Centre, University of Gothenburg, SE-40530, Gothenburg, Sweden.,Institut de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, 08028 Barcelona, Spain.,BioNMR Laboratory, Inorganic and Organic Chemistry Department, Organic Chemistry Section, University of Barcelona, Parc Cientific de Barcelona, 08028 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Parc Cientific de Barcelona, 08028 Barcelona, Spain.,XALOC beamline, ALBA synchrotron (CELLS), 08290 Cerdanyola del Valles, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF125
A, B
232Homo sapiensMutation(s): 0 
Gene Names: RNF125
EC: 2.3.2.27
Find proteins for Q96EQ8 (Homo sapiens)
Go to Gene View: RNF125
Go to UniProtKB:  Q96EQ8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.670α = 90.00
b = 52.320β = 90.00
c = 73.970γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release