PDBsum entry 5aht

Isomerase

PDB id: 5aht

Contents

Protein chain

43 a.a.

PDB id:

5aht

Name:

Isomerase

Title:

Third ww domain from the e3 ubiquitin-protein ligase nedd4

Structure:

E3 ubiquitin-protein ligase nedd4. Chain: a. Fragment: ww3, unp residues 838-877. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta plyss.

NMR struc:

15 models

Authors:

V.Panwalkar,J.Lecher,A.Dingley

Key ref:

V.Panwalkar et al. (2016). The Nedd4-1 WW Domain Recognizes the PY Motif Peptide through Coupled Folding and Binding Equilibria. Biochemistry, 55, 659-674. PubMed id: 26685112 DOI: 10.1021/acs.biochem.5b01028

Date:

09-Feb-15 Release date: 27-Jan-16

Protein chain

P46934  (NEDD4_HUMAN) -  E3 ubiquitin-protein ligase NEDD4 from Homo sapiens

Seq: 1319 a.a.

Struc: 43 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.2.26 - HECT-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1021/acs.biochem.5b01028

Biochemistry 55:659-674 (2016)

PubMed id: 26685112

The Nedd4-1 WW Domain Recognizes the PY Motif Peptide through Coupled Folding and Binding Equilibria.

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

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.