5YWR

Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report



Literature

Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications.

Behera, A.P.Naskar, P.Agarwal, S.Banka, P.A.Poddar, A.Datta, A.B.

(2018) Biochem J 475: 1569-1582

  • DOI: 10.1042/BCJ20170909
  • Primary Citation of Related Structures:  
    5YWR

  • PubMed Abstract: 
  • RING ( R eally I nteresting N ew G ene) domains in ubiquitin RING E3 ligases exclusively engage ubiquitin (Ub)-loaded E2s to facilitate ubiquitination of their substrates. Despite such specificity, all RINGs characteriz ...

    RING ( R eally I nteresting N ew G ene) domains in ubiquitin RING E3 ligases exclusively engage ubiquitin (Ub)-loaded E2s to facilitate ubiquitination of their substrates. Despite such specificity, all RINGs characterized till date bind unloaded E2s with dissociation constants ( K d s) in the micromolar to the sub-millimolar range. Here, we show that the RING domain of E3 ligase ZNRF1, an essential E3 ligase implicated in diverse cellular pathways, binds Ube2N with a K d of ∼50 nM. This high-affinity interaction is exclusive for Ube2N as ZNRF1 interacts with Ube2D2 with a K d of ∼1 µM, alike few other E3s. The crystal structure of ZNRF1 C-terminal domain in complex with Ube2N coupled with mutational analyses reveals the molecular basis of this unusual affinity. We further demonstrate that the ubiquitination efficiency of ZNRF1 : E2 pairs correlates with their affinity. Intriguingly, as a consequence of its high E2 affinity, an excess of ZNRF1 inhibits Ube2N-mediated ubiquitination at concentrations ≥500 nM instead of showing enhanced ubiquitination. This suggests a novel mode of activity regulation of E3 ligases and emphasizes the importance of E3-E2 balance for the optimum activity. Based on our results, we propose that overexpression-based functional analyses on E3 ligases such as ZNRF1 must be approached with caution as enhanced cellular levels might result in aberrant modification activity.


    Organizational Affiliation

    Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India ajit@jcbose.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NA152Homo sapiensMutation(s): 0 
Gene Names: UBE2NBLU
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS  P61088
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ZNRF1B89Homo sapiensMutation(s): 0 
Gene Names: ZNRF1NIN283
EC: 2.3.2.27
Find proteins for Q8ND25 (Homo sapiens)
Explore Q8ND25 
Go to UniProtKB:  Q8ND25
NIH Common Fund Data Resources
PHAROS  Q8ND25
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.43α = 90
b = 59.548β = 90
c = 94.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
pointlessdata scaling
SHELXDphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome Trust-DBT India AllianceIndia500241/Z/11/Z

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release