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PDBsum entry 1i5h

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protein Protein-protein interface(s) links
Ligase PDB id
1i5h
Jmol
Contents
Protein chains
50 a.a. *
17 a.a. *
* Residue conservation analysis
PDB id:
1i5h
Name: Ligase
Title: Solution structure of the rnedd4 wwiii domain-renac bp2 peptide complex
Structure: Ubiquitin ligase nedd4. Chain: w. Fragment: wwiii domain. Synonym: rnedd4. Engineered: yes. Amiloride-sensitive sodium channel beta-subunit. Chain: b. Synonym: renac bp2 peptide. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: an identical peptide was made synthetically using standard f-moc chemistry for nmr samples requiring unlabeled bp2 peptide.
NMR struc: 15 models
Authors: V.Kanelis,D.Rotin,J.D.Forman-Kay
Key ref:
V.Kanelis et al. (2001). Solution structure of a Nedd4 WW domain-ENaC peptide complex. Nat Struct Biol, 8, 407-412. PubMed id: 11323714 DOI: 10.1038/87562
Date:
27-Feb-01     Release date:   02-May-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q62940  (NEDD4_RAT) -  E3 ubiquitin-protein ligase NEDD4
Seq:
Struc:
 
Seq:
Struc:
887 a.a.
50 a.a.*
Protein chain
Pfam   ArchSchema ?
P37090  (SCNNB_RAT) -  Amiloride-sensitive sodium channel subunit beta
Seq:
Struc:
 
Seq:
Struc:
638 a.a.
17 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
DOI no: 10.1038/87562 Nat Struct Biol 8:407-412 (2001)
PubMed id: 11323714  
 
 
Solution structure of a Nedd4 WW domain-ENaC peptide complex.
V.Kanelis, D.Rotin, J.D.Forman-Kay.
 
  ABSTRACT  
 
Nedd4 is a ubiquitin protein ligase composed of a C2 domain, three (or four) WW domains and a ubiquitin ligase Hect domain. Nedd4 was demonstrated to bind the epithelial sodium channel (alphabetagammaENaC), by association of its WW domains with PY motifs (XPPXY) present in each ENaC subunit, and to regulate the cell surface stability of the channel. The PY motif of betaENaC is deleted or mutated in Liddle syndrome, a hereditary form of hypertension caused by elevated ENaC activity. Here we report the solution structure of the third WW domain of Nedd4 complexed to the PY motif-containing region of betaENaC (TLPIPGTPPPNYDSL, referred to as betaP2). A polyproline type II helical conformation is adopted by the PPPN sequence. Unexpectedly, the C-terminal sequence YDSL forms a helical turn and both the tyrosine and the C-terminal leucine contact the WW domain. This is unlike other proline-rich peptides complexed to WW domains, which bind in an extended conformation and lack molecular interactions with residues C-terminal to the tyrosine or the structurally equivalent residue in non-PY motif WW domain targets. The Nedd4 WW domain-ENaC betaP2 peptide structure expands our understanding of the mechanisms involved in WW domain-ligand recognition and the molecular basis of Liddle syndrome.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The rNedd4 WWIII -rENaC P2 peptide binding interface. Colors are as in Fig. 1 with the exception that all WW domain side chains in the binding site are in cyan.
Figure 3.
Figure 3. Surface representations of WW domain-ligand complexes. Molecular surfaces of the WW domains are shown with blue and red representing positive and negative electrostatic potential, respectively. Ligands are shown as ribbons with backbone in green and side chains of conserved residues in each motif (PY motif and pS-P) in yellow. a, rNedd4 WWIII domain -rENaC P2 complex. A few WW domain residues involved in binding are indicated. b, Pin1 WW domain -pS-P peptide complex (PDB code 1F8A)7. c, Dystrophin - -dystroglycan complex (PDB code 1EG4)25. A portion of the EF hand domain of dystrophin involved in -dystroglycan binding and contacting the WW domain is shown in gray. All figures generated using MOLMOL54.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 407-412) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20972579 D.Rotin, and O.Staub (2011).
Role of the ubiquitin system in regulating ion transport.
  Pflugers Arch, 461, 1.  
21332354 J.H.Hurley, and H.Stenmark (2011).
Molecular mechanisms of ubiquitin-dependent membrane traffic.
  Annu Rev Biophys, 40, 119-142.  
20026598 F.Fouladkou, C.Lu, C.Jiang, L.Zhou, Y.She, J.R.Walls, H.Kawabe, N.Brose, R.M.Henkelman, A.Huang, B.G.Bruneau, and D.Rotin (2010).
The ubiquitin ligase Nedd4-1 is required for heart development and is a suppressor of thrombospondin-1.
  J Biol Chem, 285, 6770-6780.  
20159161 J.Juraszek, and P.G.Bolhuis (2010).
(Un)Folding mechanisms of the FBP28 WW domain in explicit solvent revealed by multiple rare event simulation methods.
  Biophys J, 98, 646-656.  
20880397 M.K.Mansley, and S.M.Wilson (2010).
Effects of nominally selective inhibitors of the kinases PI3K, SGK1 and PKB on the insulin-dependent control of epithelial Na+ absorption.
  Br J Pharmacol, 161, 571-588.  
20937913 P.A.Chong, H.Lin, J.L.Wrana, and J.D.Forman-Kay (2010).
Coupling of tandem Smad ubiquitination regulatory factor (Smurf) WW domains modulates target specificity.
  Proc Natl Acad Sci U S A, 107, 18404-18409.
PDB code: 2kxq
19953087 A.Persaud, P.Alberts, E.M.Amsen, X.Xiong, J.Wasmuth, Z.Saadon, C.Fladd, J.Parkinson, and D.Rotin (2009).
Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays.
  Mol Syst Biol, 5, 333.  
20007785 C.T.Wong Po Foo, J.S.Lee, W.Mulyasasmita, A.Parisi-Amon, and S.C.Heilshorn (2009).
Two-component protein-engineered physical hydrogels for cell encapsulation.
  Proc Natl Acad Sci U S A, 106, 22067-22072.  
19125695 P.J.Plant, J.Correa, N.Goldenberg, J.Bain, and J.Batt (2009).
The inositol phosphatase MTMR4 is a novel target of the ubiquitin ligase Nedd4.
  Biochem J, 419, 57-63.  
19114059 R.N.Harty (2009).
No exit: targeting the budding process to inhibit filovirus replication.
  Antiviral Res, 81, 189-197.  
19592703 X.Huang, M.Beullens, J.Zhang, Y.Zhou, E.Nicolaescu, B.Lesage, Q.Hu, J.Wu, M.Bollen, and Y.Shi (2009).
Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21).
  J Biol Chem, 284, 25375-25387.
PDB code: 2jxw
19028681 Y.Park, S.K.Yoon, and J.B.Yoon (2009).
The HECT Domain of TRIP12 Ubiquitinates Substrates of the Ubiquitin Fusion Degradation Pathway.
  J Biol Chem, 284, 1540-1549.  
18398334 E.Rossi, E.Farnetti, A.Debonneville, D.Nicoli, C.Grasselli, G.Regolisti, A.Negro, F.Perazzoli, B.Casali, F.Mantero, and O.Staub (2008).
Liddle's syndrome caused by a novel missense mutation (P617L) of the epithelial sodium channel beta subunit.
  J Hypertens, 26, 921-927.  
18562292 F.Fouladkou, T.Landry, H.Kawabe, A.Neeb, C.Lu, N.Brose, V.Stambolic, and D.Rotin (2008).
The ubiquitin ligase Nedd4-1 is dispensable for the regulation of PTEN stability and localization.
  Proc Natl Acad Sci U S A, 105, 8585-8590.  
18321968 H.Y.Chung, E.Morita, U.von Schwedler, B.Müller, H.G.Kräusslich, and W.I.Sundquist (2008).
NEDD4L overexpression rescues the release and infectivity of human immunodeficiency virus type 1 constructs lacking PTAP and YPXL late domains.
  J Virol, 82, 4884-4897.  
18174164 R.Kabra, K.K.Knight, R.Zhou, and P.M.Snyder (2008).
Nedd4-2 induces endocytosis and degradation of proteolytically cleaved epithelial Na+ channels.
  J Biol Chem, 283, 6033-6039.  
17074801 B.Ing, A.Shteiman-Kotler, M.Castelli, P.Henry, Y.Pak, B.Stewart, G.L.Boulianne, and D.Rotin (2007).
Regulation of Commissureless by the ubiquitin ligase DNedd4 is required for neuromuscular synaptogenesis in Drosophila melanogaster.
  Mol Cell Biol, 27, 481-496.  
17437719 B.Morales, X.Ramirez-Espain, A.Z.Shaw, P.Martin-Malpartida, F.Yraola, E.Sánchez-Tilló, C.Farrera, A.Celada, M.Royo, and M.J.Macias (2007).
NMR structural studies of the ItchWW3 domain reveal that phosphorylation at T30 inhibits the interaction with PPxY-containing ligands.
  Structure, 15, 473-483.
PDB codes: 2jo9 2joc
17605762 C.Lu, S.Pribanic, A.Debonneville, C.Jiang, and D.Rotin (2007).
The PY motif of ENaC, mutated in Liddle syndrome, regulates channel internalization, sorting and mobilization from subapical pool.
  Traffic, 8, 1246-1264.  
17502622 J.D.Kulman, J.E.Harris, L.Xie, and E.W.Davie (2007).
Proline-rich Gla protein 2 is a cell-surface vitamin K-dependent protein that binds to the transcriptional coactivator Yes-associated protein.
  Proc Natl Acad Sci U S A, 104, 8767-8772.  
17656366 M.D.Jennings, R.T.Blankley, M.Baron, A.P.Golovanov, and J.M.Avis (2007).
Specificity and autoregulation of Notch binding by tandem WW domains in suppressor of Deltex.
  J Biol Chem, 282, 29032-29042.
PDB code: 2jmf
17686488 M.Meiyappan, G.Birrane, and J.A.Ladias (2007).
Structural basis for polyproline recognition by the FE65 WW domain.
  J Mol Biol, 372, 970-980.
PDB codes: 2ho2 2idh 2oei
17932789 O.Gileadi, S.Knapp, W.H.Lee, B.D.Marsden, S.Müller, F.H.Niesen, K.L.Kavanagh, L.J.Ball, F.von Delft, D.A.Doyle, U.C.Oppermann, and M.Sundström (2007).
The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.
  J Struct Funct Genomics, 8, 107-119.  
17551511 R.Gupta, B.Kus, C.Fladd, J.Wasmuth, R.Tonikian, S.Sidhu, N.J.Krogan, J.Parkinson, and D.Rotin (2007).
Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
  Mol Syst Biol, 3, 116.  
16460280 J.Loffing, S.Y.Flores, and O.Staub (2006).
Sgk kinases and their role in epithelial transport.
  Annu Rev Physiol, 68, 461-490.  
16606443 J.R.Hesselberth, J.P.Miller, A.Golob, J.E.Stajich, G.A.Michaud, and S.Fields (2006).
Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins.
  Genome Biol, 7, R30.  
16807295 M.Jäger, Y.Zhang, J.Bieschke, H.Nguyen, M.Dendle, M.E.Bowman, J.P.Noel, M.Gruebele, and J.W.Kelly (2006).
Structure-function-folding relationship in a WW domain.
  Proc Natl Acad Sci U S A, 103, 10648-10653.
PDB codes: 1zcn 2f21
16641086 P.A.Chong, H.Lin, J.L.Wrana, and J.D.Forman-Kay (2006).
An expanded WW domain recognition motif revealed by the interaction between Smad7 and the E3 ubiquitin ligase Smurf2.
  J Biol Chem, 281, 17069-17075.
PDB code: 2djy
17110928 T.Wegierski, K.Hill, M.Schaefer, and G.Walz (2006).
The HECT ubiquitin ligase AIP4 regulates the cell surface expression of select TRP channels.
  EMBO J, 25, 5659-5669.  
16531238 V.Kanelis, M.C.Bruce, N.R.Skrynnikov, D.Rotin, and J.D.Forman-Kay (2006).
Structural determinants for high-affinity binding in a Nedd4 WW3* domain-Comm PY motif complex.
  Structure, 14, 543-553.
PDB code: 2ez5
16613846 X.Liang, K.W.Peters, M.B.Butterworth, and R.A.Frizzell (2006).
14-3-3 isoforms are induced by aldosterone and participate in its regulation of epithelial sodium channels.
  J Biol Chem, 281, 16323-16332.  
16533840 Y.Mu, L.Nordenskiöld, and J.P.Tam (2006).
Folding, misfolding, and amyloid protofibril formation of WW domain FBP28.
  Biophys J, 90, 3983-3992.  
16203727 A.Staruschenko, O.Pochynyuk, and J.D.Stockand (2005).
Regulation of epithelial Na+ channel activity by conserved serine/threonine switches within sorting signals.
  J Biol Chem, 280, 39161-39167.  
15955809 B.Kus, A.Gajadhar, K.Stanger, R.Cho, W.Sun, N.Rouleau, T.Lee, D.Chan, C.Wolting, A.Edwards, R.Bosse, and D.Rotin (2005).
A high throughput screen to identify substrates for the ubiquitin ligase Rsp5.
  J Biol Chem, 280, 29470-29478.  
15800888 J.F.Espinosa, F.A.Syud, and S.H.Gellman (2005).
An autonomously folding beta-hairpin derived from the human YAP65 WW domain: attempts to define a minimum ligand-binding motif.
  Biopolymers, 80, 303-311.  
15880548 L.J.Ball, R.Kühne, J.Schneider-Mergener, and H.Oschkinat (2005).
Recognition of Proline-Rich Motifs by Protein-Protein-Interaction Domains.
  Angew Chem Int Ed Engl, 44, 2852-2869.  
16177782 M.Socolich, S.W.Lockless, W.P.Russ, H.Lee, K.H.Gardner, and R.Ranganathan (2005).
Evolutionary information for specifying a protein fold.
  Nature, 437, 512-518.
PDB code: 1ymz
16341092 M.Wang, and C.M.Pickart (2005).
Different HECT domain ubiquitin ligases employ distinct mechanisms of polyubiquitin chain synthesis.
  EMBO J, 24, 4324-4333.  
16055720 R.J.Ingham, K.Colwill, C.Howard, S.Dettwiler, C.S.Lim, J.Yu, K.Hersi, J.Raaijmakers, G.Gish, G.Mbamalu, L.Taylor, B.Yeung, G.Vassilovski, M.Amin, F.Chen, L.Matskova, G.Winberg, I.Ernberg, R.Linding, P.O'donnell, A.Starostine, W.Keller, P.Metalnikov, C.Stark, and T.Pawson (2005).
WW domains provide a platform for the assembly of multiprotein networks.
  Mol Cell Biol, 25, 7092-7106.  
16172119 S.Michlig, M.Harris, J.Loffing, B.C.Rossier, and D.Firsov (2005).
Progesterone down-regulates the open probability of the amiloride-sensitive epithelial sodium channel via a Nedd4-2-dependent mechanism.
  J Biol Chem, 280, 38264-38270.  
15677482 T.Ichimura, H.Yamamura, K.Sasamoto, Y.Tominaga, M.Taoka, K.Kakiuchi, T.Shinkawa, N.Takahashi, S.Shimada, and T.Isobe (2005).
14-3-3 proteins modulate the expression of epithelial Na+ channels by phosphorylation-dependent interaction with Nedd4-2 ubiquitin ligase.
  J Biol Chem, 280, 13187-13194.  
16177795 W.P.Russ, D.M.Lowery, P.Mishra, M.B.Yaffe, and R.Ranganathan (2005).
Natural-like function in artificial WW domains.
  Nature, 437, 579-583.  
15180901 H.Mira, M.Vilar, V.Esteve, M.Martinell, M.J.Kogan, E.Giralt, D.Salom, I.Mingarro, L.Peñarrubia, and E.Pérez-Payá (2004).
Ionic self-complementarity induces amyloid-like fibril formation in an isolated domain of a plant copper metallochaperone protein.
  BMC Struct Biol, 4, 7.  
14990566 J.Nie, S.S.Li, and C.J.McGlade (2004).
A novel PTB-PDZ domain interaction mediates isoform-specific ubiquitylation of mammalian Numb.
  J Biol Chem, 279, 20807-20815.  
15173166 O.Y.Fedoroff, S.A.Townson, A.P.Golovanov, M.Baron, and J.M.Avis (2004).
The structure and dynamics of tandem WW domains in a negative regulator of notch signaling, Suppressor of deltex.
  J Biol Chem, 279, 34991-35000.
PDB code: 1tk7
15133021 Y.Kato, K.Nagata, M.Takahashi, L.Lian, J.J.Herrero, M.Sudol, and M.Tanokura (2004).
Common mechanism of ligand recognition by group II/III WW domains: redefining their functional classification.
  J Biol Chem, 279, 31833-31841.  
12697834 A.Vecchione, A.Marchese, P.Henry, D.Rotin, and A.Morrione (2003).
The Grb10/Nedd4 complex regulates ligand-induced ubiquitination and stability of the insulin-like growth factor I receptor.
  Mol Cell Biol, 23, 3363-3372.  
12651955 H.Nguyen, M.Jager, A.Moretto, M.Gruebele, and J.W.Kelly (2003).
Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation.
  Proc Natl Acad Sci U S A, 100, 3948-3953.  
12592019 L.Otte, U.Wiedemann, B.Schlegel, J.R.Pires, M.Beyermann, P.Schmieder, G.Krause, R.Volkmer-Engert, J.Schneider-Mergener, and H.Oschkinat (2003).
WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains.
  Protein Sci, 12, 491-500.  
12654927 P.C.Henry, V.Kanelis, M.C.O'Brien, B.Kim, I.Gautschi, J.Forman-Kay, L.Schild, and D.Rotin (2003).
Affinity and specificity of interactions between Nedd4 isoforms and the epithelial Na+ channel.
  J Biol Chem, 278, 20019-20028.  
12897071 R.E.Booth, Q.Tong, J.Medina, P.M.Snyder, P.Patel, and J.D.Stockand (2003).
A region directly following the second transmembrane domain in gamma ENaC is required for normal channel gating.
  J Biol Chem, 278, 41367-41379.  
12767128 S.L.Lam, and V.L.Hsu (2003).
NMR identification of left-handed polyproline type II helices.
  Biopolymers, 69, 270-281.  
12165468 A.Myat, P.Henry, V.McCabe, L.Flintoft, D.Rotin, and G.Tear (2002).
Drosophila Nedd4, a ubiquitin ligase, is recruited by Commissureless to control cell surface levels of the roundabout receptor.
  Neuron, 35, 447-459.  
11773057 D.Hanwell, T.Ishikawa, R.Saleki, and D.Rotin (2002).
Trafficking and cell surface stability of the epithelial Na+ channel expressed in epithelial Madin-Darby canine kidney cells.
  J Biol Chem, 277, 9772-9779.  
12093811 E.Hendron, P.Patel, M.Hausenfluke, N.Gamper, M.S.Shapiro, R.E.Booth, and J.D.Stockand (2002).
Identification of cytoplasmic domains within the epithelial Na+ channel reactive at the plasma membrane.
  J Biol Chem, 277, 34480-34488.  
11805112 H.Shi, C.Asher, A.Chigaev, Y.Yung, E.Reuveny, R.Seger, and H.Garty (2002).
Interactions of beta and gamma ENaC with Nedd4 can be facilitated by an ERK-mediated phosphorylation.
  J Biol Chem, 277, 13539-13547.  
11859027 J.J.Chung, S.Shikano, Y.Hanyu, and M.Li (2002).
Functional diversity of protein C-termini: more than zipcoding?
  Trends Cell Biol, 12, 146-150.  
11751914 Y.Kato, M.Ito, K.Kawai, K.Nagata, and M.Tanokura (2002).
Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building.
  J Biol Chem, 277, 10173-10177.  
11742982 C.Debonneville, S.Y.Flores, E.Kamynina, P.J.Plant, C.Tauxe, M.A.Thomas, C.Münster, A.Chraïbi, J.H.Pratt, J.D.Horisberger, D.Pearce, J.Loffing, and O.Staub (2001).
Phosphorylation of Nedd4-2 by Sgk1 regulates epithelial Na(+) channel cell surface expression.
  EMBO J, 20, 7052-7059.  
11687613 N.Ferguson, C.M.Johnson, M.Macias, H.Oschkinat, and A.Fersht (2001).
Ultrafast folding of WW domains without structured aromatic clusters in the denatured state.
  Proc Natl Acad Sci U S A, 98, 13002-13007.  
11687614 N.Ferguson, J.R.Pires, F.Toepert, C.M.Johnson, Y.P.Pan, R.Volkmer-Engert, J.Schneider-Mergener, V.Daggett, H.Oschkinat, and A.Fersht (2001).
Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.
  Proc Natl Acad Sci U S A, 98, 13008-13013.
PDB code: 1k5r
11598133 N.Pham, and D.Rotin (2001).
Nedd4 regulates ubiquitination and stability of the guanine-nucleotide exchange factor CNrasGEF.
  J Biol Chem, 276, 46995-47003.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.