5AHT

Third WW domain from the E3 ubiquitin-protein ligase NEDD4

Summary for 5AHT

• Entry DOI: 10.2210/pdb5aht/pdb
• NMR Information: BMRB: 25349
• Descriptor: E3 UBIQUITIN-PROTEIN LIGASE NEDD4 (1 entity in total)
• Functional Keywords: isomerase, ww3, protein-peptide complex, protein dynamics, proein structure
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Cytoplasm : P46934
• Total number of polymer chains: 1
• Total formula weight: 4971.61

Authors

Panwalkar, V.,Lecher, J.,Dingley, A. (deposition date: 2015-02-09, release date: 2016-01-27, Last modification date: 2024-01-31)

Primary citation

Panwalkar, V.,Neudecker, P.,Schmitz, M.,Lecher, J.,Schulte, M.,Medini, K.,Stoldt, M.,Brimble, M.A.,Willbold, D.,Dingley, A.J.
The Nedd4-1 Ww Domain Recognizes the Py Motif Peptide Through Coupled Folding and Binding Equilibria.
Biochemistry, 55:659-, 2016

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 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.

PubMed: 26685112
DOI: 10.1021/ACS.BIOCHEM.5B01028

Experimental method

SOLUTION NMR