5AHT

Third WW domain from the E3 ubiquitin-protein ligase NEDD4


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: LOWEST ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Nedd4-1 Ww Domain Recognizes the Py Motif Peptide Through Coupled Folding and Binding Equilibria.

Panwalkar, V.Neudecker, P.Schmitz, M.Lecher, J.Schulte, M.Medini, K.Stoldt, M.Brimble, M.A.Willbold, D.Dingley, A.J.

(2016) Biochemistry 55: 659

  • DOI: 10.1021/acs.biochem.5b01028

  • PubMed Abstract: 
  • The four WW domains of human Nedd4-1 (neuronal precursor cell expressed developmentally downregulated gene 4-1) interact with the PPxY (PY) motifs of the human epithelial Na(+) channel (hENaC) subunits, with the third WW domain (WW3*) showing the hig ...

    The four WW domains of human Nedd4-1 (neuronal precursor cell expressed developmentally downregulated gene 4-1) interact with the PPxY (PY) motifs of the human epithelial Na(+) channel (hENaC) subunits, with the third WW domain (WW3*) showing the highest affinity. We have shown previously that the α-hENaC PY motif binding interface of WW3* undergoes conformational exchange on the millisecond time scale, indicating that conformational sampling plays a role in peptide recognition. To further understand this role, the structure and dynamics of hNedd4-1 WW3* were investigated. The nuclear Overhauser effect-derived structure of apo-WW3* resembles the domain in complex with the α-hENaC peptide, although particular side chain conformations change upon peptide binding, which was further investigated by molecular dynamics simulations. Model-free analysis of the (15)N nuclear magnetic resonance spin relaxation data showed that the apo and peptide-bound states of WW3* have similar backbone picosecond to nanosecond time scale dynamics. However, apo-WW3* exhibits pronounced chemical exchange on the millisecond time scale that is quenched upon peptide binding. (1)HN and (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments at various temperatures revealed that apo-WW3* exists in an equilibrium between the natively folded peptide binding-competent state and a random coil-like denatured state. The thermodynamics of the folding equilibrium was determined by fitting a thermal denaturation profile monitored by circular dichroism spectroscopy in combination with the CPMG data, leading to the conclusion that the unfolded state is populated to ∼ 20% at 37 °C. These results show that the binding of the hNedd4-1 WW3* domain to α-hENaC is coupled to the folding equilibrium.


    Organizational Affiliation

    ICS-6 (Strukturbiochemie), Forschungszentrum Jülich , 52425 Jülich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE NEDD4
A
43Homo sapiensMutation(s): 0 
Gene Names: NEDD4 (KIAA0093, NEDD4-1)
EC: 2.3.2.26
Find proteins for P46934 (Homo sapiens)
Go to Gene View: NEDD4
Go to UniProtKB:  P46934
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: LOWEST ENERGY 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references