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119  structures 357  species 3  interactions 8927  sequences 403  architectures

Family: WW (PF00397)

Summary: WW domain

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WW domain Edit Wikipedia article

WW domain
PDB 1pin EBI.jpg
Structure of the human mitotic rotamase Pin1.[1]
Identifiers
Symbol WW
Pfam PF00397
InterPro IPR001202
PROSITE PDOC50020
SCOP 1pin
SUPERFAMILY 1pin
CDD cd00201

The WW domain,[2] (also known as the rsp5-domain[3] or WWP repeating motif[4]) is a modular protein domain that mediates specific interactions with protein ligands. This domain is found in a number of unrelated signaling and structural proteins and may be repeated up to four times in some proteins.[2][4][3][5] Apart from binding preferentially to proteins that are proline-rich, with particular proline-motifs, [AP]-P-P-[AP]-Y, some WW domains bind to phosphoserine- phosphothreonine-containing motifs.[6]

Structure and ligands[edit]

The WW domain is one of the smallest protein modules, composed of only 40 amino acids, which mediates specific protein-protein interactions with short proline-rich or proline-containing motifs.[6] Named after the presence of two conserved tryptophans (W), which are spaced 20-22 amino acids apart within the sequence,[2] the WW domain folds into a meandering triple-stranded beta sheet.[7] The identification of the WW domain was facilitated by the analysis of two splice isoforms of YAP gene product, named YAP1-1 and YAP1-2, which differed by the presence of an extra 38 amino acids. These extra amino acids are encoded by a spliced-in exon and represent the second WW domain in YAP1-2 isoform.[2][8]

The first structure of the WW domain was determined in solution by NMR approach.[7] It represented the WW domain of human YAP in complex with peptide ligand containing Proline-Proline-x–Tyrosine (PPxY where x = any amino acid) consensus motif.[6][7] Recently, the YAP WW domain structure in complex with SMAD-derived, PPxY motif-containing peptide was further refined.[9] Apart from the PPxY motif, certain WW domains recognize LPxY motif (where L is Leucine),[10] and several WW domains bind to phospho-Serine-Proline (p-SP) or phospho-Threonine-Proline (p-ST) motifs in a phospho-dependent manner.[11] Structures of these WW domain complexes confirmed molecular details of phosphorylation-regulated interactions.[1][12] There are also WW domains that interact with polyprolines that are flanked by arginine residues or interrupted by leucine residues, but they do not contain aromatic amino acids.[13][14]

Signaling function[edit]

The WW domain is known to mediate regulatory protein complexes in various signaling networks, including the Hippo signaling pathway.[15] The importance of WW domain-mediated complexes in signaling was underscored by the characterization of genetic syndromes that are caused by loss-of-function point mutations in the WW domain or its cognate ligand. These syndromes are Golabi-Ito-Hall syndrome of intellectual disability caused by missense mutation in a WW domain[16][17] and Liddle syndrome of hypertension caused by point mutations within PPxY motif.[18][19]

Examples[edit]

A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein; vertebrate YAP protein, substrate of LATS1 and LATS2 serine-theronine kinases of the Hippo tumor suppressor pathway; Mus musculus (Mouse) NEDD4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD4 in its molecular organization; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in brain; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.

In 2004, the first comprehensive protein-peptide interaction map for a human modular domain was reported using individually expressed WW domains and genome predicted, PPxY-containing synthetic peptides.[20] At present in the human proteome, 98 WW domains[21] and more than 2000 PPxY-containing peptides,[17] have been identified from sequence analysis of the genome.

Inhibitor[edit]

YAP is a WW domain-containing protein that functions as a potent oncogene.[2][22] Its WW domains must be intact for YAP to act as a transcriptional co-activator that induces expression of proliferative genes.[23] Recent study has shown that endohedral metallofullerenol, a compound that was originally developed as a contrasting agent for MRI (magnetic resonance imaging), has antineoplastic properties.[24] Via molecular dynamic simulations, the ability of this compound to outcompete proline-rich peptides and bind effectively to the WW domain of YAP was documented.[25] Endotheral metallofullerenol may represent a lead compound for the development of therapies for cancer patients who harbor amplified or overexpressed YAP.[25][26]

In the study of protein folding[edit]

Because of its small size and well-defined structure, the WW domain became a favorite subject of protein folding studies.[27][28][29] Among these studies, the work of Rama Ranganathan [30][31] and David E. Shaw are notable.[32][33] Ranganathan’s team has shown that a simple statistical energy function, which identifies co-evolution between amino acid residues within the WW domain, is necessary and sufficient to specify sequence that folds into native structure.[31] Using such an algorithm, he and his team synthesized libraries of artificial WW domains that functioned in a very similar manner to their natural counterparts, recognizing class-specific proline-rich ligand peptides,[30] The Shaw laboratory developed a specialized machine that allowed elucidation of the atomic level behavior of the WW domain on a biologically relevant time scale.[32] He and his team employed equilibrium simulations of a WW domain and identified seven unfolding and eight folding events that follow the same folding route.[33]

References[edit]

  1. ^ a b PDB 1PIN; Ranganathan R, Lu KP, Hunter T, Noel JP (June 1997). "Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent". Cell 89 (6): 875–86. doi:10.1016/S0092-8674(00)80273-1. PMID 9200606. 
  2. ^ a b c d e Bork P, Sudol M (December 1994). "The WW domain: a signalling site in dystrophin?". Trends Biochem. Sci. 19 (12): 531–3. doi:10.1016/0968-0004(94)90053-1. PMID 7846762. 
  3. ^ a b Hofmann K, Bucher P (January 1995). "The rsp5-domain is shared by proteins of diverse functions". FEBS Lett. 358 (2): 153–7. doi:10.1016/0014-5793(94)01415-W. PMID 7828727. 
  4. ^ a b André B, Springael JY (December 1994). "WWP, a new amino acid motif present in single or multiple copies in various proteins including dystrophin and the SH3-binding Yes-associated protein YAP65". Biochem. Biophys. Res. Commun. 205 (2): 1201–5. doi:10.1006/bbrc.1994.2793. PMID 7802651. 
  5. ^ Sudol M, Chen HI, Bougeret C, Einbond A, Bork P (August 1995). "Characterization of a novel protein-binding module--the WW domain". FEBS Lett. 369 (1): 67–71. doi:10.1016/0014-5793(95)00550-S. PMID 7641887. 
  6. ^ a b c Chen HI, Sudol M (August 1995). "The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules". Proc. Natl. Acad. Sci. U.S.A. 92 (17): 7819–23. Bibcode:1995PNAS...92.7819C. doi:10.1073/pnas.92.17.7819. PMC 41237. PMID 7644498. 
  7. ^ a b c Macias MJ, Hyvönen M, Baraldi E, Schultz J, Sudol M, Saraste M, Oschkinat H (August 1996). "Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide". Nature 382 (6592): 646–9. Bibcode:1996Natur.382..646M. doi:10.1038/382646a0. PMID 8757138. 
  8. ^ Sudol M, Bork P, Einbond A, Kastury K, Druck T, Negrini M, Huebner K, Lehman D (June 1995). "Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain". J. Biol. Chem. 270 (24): 14733–41. doi:10.1074/jbc.270.24.14733. PMID 7782338. 
  9. ^ Aragón E, Goerner N, Xi Q, Gomes T, Gao S, Massagué J, Macias MJ (October 2012). "Structural basis for the versatile interactions of Smad7 with regulator WW domains in TGF-β Pathways". Structure 20 (10): 1726–36. doi:10.1016/j.str.2012.07.014. PMC 3472128. PMID 22921829. 
  10. ^ Bruce MC, Kanelis V, Fouladkou F, Debonneville A, Staub O, Rotin D (October 2008). "Regulation of Nedd4-2 self-ubiquitination and stability by a PY motif located within its HECT-domain". Biochem. J. 415 (1): 155–63. doi:10.1042/BJ20071708. PMID 18498246. 
  11. ^ Lu PJ, Zhou XZ, Shen M, Lu KP (February 1999). "Function of WW domains as phosphoserine- or phosphothreonine-binding modules". Science 283 (5406): 1325–8. Bibcode:1999Sci...283.1325L. doi:10.1126/science.283.5406.1325. PMID 10037602. 
  12. ^ Verdecia MA, Bowman ME, Lu KP, Hunter T, Noel JP (August 2000). "Structural basis for phosphoserine-proline recognition by group IV WW domains". Nat. Struct. Biol. 7 (8): 639–43. doi:10.1038/77929. PMID 10932246. 
  13. ^ Bedford MT, Sarbassova D, Xu J, Leder P, Yaffe MB (April 2000). "A novel pro-Arg motif recognized by WW domains". J. Biol. Chem. 275 (14): 10359–69. doi:10.1074/jbc.275.14.10359. PMID 10744724. 
  14. ^ Ermekova KS, Zambrano N, Linn H, Minopoli G, Gertler F, Russo T, Sudol M (December 1997). "The WW domain of neural protein FE65 interacts with proline-rich motifs in Mena, the mammalian homolog of Drosophila enabled". J. Biol. Chem. 272 (52): 32869–77. doi:10.1074/jbc.272.52.32869. PMID 9407065. 
  15. ^ Sudol M, Harvey KF (November 2010). "Modularity in the Hippo signaling pathway". Trends Biochem. Sci. 35 (11): 627–33. doi:10.1016/j.tibs.2010.05.010. PMID 20598891. 
  16. ^ Lubs H, Abidi FE, Echeverri R, Holloway L, Meindl A, Stevenson RE, Schwartz CE (June 2006). "Golabi-Ito-Hall syndrome results from a missense mutation in the WW domain of the PQBP1 gene". J. Med. Genet. 43 (6): e30. doi:10.1136/jmg.2005.037556. PMC 2564547. PMID 16740914. 
  17. ^ a b Tapia VE, Nicolaescu E, McDonald CB, Musi V, Oka T, Inayoshi Y, Satteson AC, Mazack V, Humbert J, Gaffney CJ, Beullens M, Schwartz CE, Landgraf C, Volkmer R, Pastore A, Farooq A, Bollen M, Sudol M (June 2010). "Y65C missense mutation in the WW domain of the Golabi-Ito-Hall syndrome protein PQBP1 affects its binding activity and deregulates pre-mRNA splicing". J. Biol. Chem. 285 (25): 19391–401. doi:10.1074/jbc.M109.084525. PMC 2885219. PMID 20410308. 
  18. ^ Schild L, Lu Y, Gautschi I, Schneeberger E, Lifton RP, Rossier BC (May 1996). "Identification of a PY motif in the epithelial Na channel subunits as a target sequence for mutations causing channel activation found in Liddle syndrome". EMBO J. 15 (10): 2381–7. PMC 450168. PMID 8665845. 
  19. ^ Staub O, Gautschi I, Ishikawa T, Breitschopf K, Ciechanover A, Schild L, Rotin D (November 1997). "Regulation of stability and function of the epithelial Na+ channel (ENaC) by ubiquitination". EMBO J. 16 (21): 6325–36. doi:10.1093/emboj/16.21.6325. PMC 1170239. PMID 9351815. 
  20. ^ Hu H, Columbus J, Zhang Y, Wu D, Lian L, Yang S, Goodwin J, Luczak C, Carter M, Chen L, James M, Davis R, Sudol M, Rodwell J, Herrero JJ (March 2004). "A map of WW domain family interactions". Proteomics 4 (3): 643–55. doi:10.1002/pmic.200300632. PMID 14997488. 
  21. ^ Sudol M, McDonald CB, Farooq A (August 2012). "Molecular insights into the WW domain of the Golabi-Ito-Hall syndrome protein PQBP1". FEBS Lett. 586 (17): 2795–9. doi:10.1016/j.febslet.2012.03.041. PMC 3413755. PMID 22710169. 
  22. ^ Huang J, Wu S, Barrera J, Matthews K, Pan D (August 2005). "The Hippo signaling pathway coordinately regulates cell proliferation and apoptosis by inactivating Yorkie, the Drosophila Homolog of YAP". Cell 122 (3): 421–34. doi:10.1016/j.cell.2005.06.007. PMID 16096061. 
  23. ^ Zhao B, Kim J, Ye X, Lai ZC, Guan KL (February 2009). "Both TEAD-binding and WW domains are required for the growth stimulation and oncogenic transformation activity of yes-associated protein". Cancer Res. 69 (3): 1089–98. doi:10.1158/0008-5472.CAN-08-2997. PMID 19141641. 
  24. ^ Kang SG, Zhou G, Yang P, Liu Y, Sun B, Huynh T, Meng H, Zhao L, Xing G, Chen C, Zhao Y, Zhou R (September 2012). "Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine". Proc. Natl. Acad. Sci. U.S.A. 109 (38): 15431–6. Bibcode:2012PNAS..10915431K. doi:10.1073/pnas.1204600109. PMC 3458392. PMID 22949663. 
  25. ^ a b Kang SG, Huynh T, Zhou R (2012). "Non-destructive inhibition of metallofullerenol Gd@C(82)(OH)(22) on WW domain: implication on signal transduction pathway". Sci Rep 2: 957. Bibcode:2012NatSR...2E.957K. doi:10.1038/srep00957. PMC 3518810. PMID 23233876. 
  26. ^ Sudol M, Shields DC, Farooq A (September 2012). "Structures of YAP protein domains reveal promising targets for development of new cancer drugs". Semin. Cell Dev. Biol. 23 (7): 827–33. doi:10.1016/j.semcdb.2012.05.002. PMC 3427467. PMID 22609812. 
  27. ^ Fuller AA, Du D, Liu F, Davoren JE, Bhabha G, Kroon G, Case DA, Dyson HJ, Powers ET, Wipf P, Gruebele M, Kelly JW (July 2009). "Evaluating beta-turn mimics as beta-sheet folding nucleators". Proc. Natl. Acad. Sci. U.S.A. 106 (27): 11067–72. Bibcode:2009PNAS..10611067F. doi:10.1073/pnas.0813012106. PMC 2708776. PMID 19541614. 
  28. ^ Jager M, Deechongkit S, Koepf EK, Nguyen H, Gao J, Powers ET, Gruebele M, Kelly JW (2008). "Understanding the mechanism of beta-sheet folding from a chemical and biological perspective". Biopolymers 90 (6): 751–8. doi:10.1002/bip.21101. PMID 18844292. 
  29. ^ Jäger M, Zhang Y, Bieschke J, Nguyen H, Dendle M, Bowman ME, Noel JP, Gruebele M, Kelly JW (July 2006). "Structure-function-folding relationship in a WW domain". Proc. Natl. Acad. Sci. U.S.A. 103 (28): 10648–53. Bibcode:2006PNAS..10310648J. doi:10.1073/pnas.0600511103. PMC 1502286. PMID 16807295. 
  30. ^ a b Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R (September 2005). "Natural-like function in artificial WW domains". Nature 437 (7058): 579–83. Bibcode:2005Natur.437..579R. doi:10.1038/nature03990. PMID 16177795. 
  31. ^ a b Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R (September 2005). "Evolutionary information for specifying a protein fold". Nature 437 (7058): 512–8. Bibcode:2005Natur.437..512S. doi:10.1038/nature03991. PMID 16177782. 
  32. ^ a b Piana S, Sarkar K, Lindorff-Larsen K, Guo M, Gruebele M, Shaw DE (January 2011). "Computational design and experimental testing of the fastest-folding β-sheet protein". J. Mol. Biol. 405 (1): 43–8. doi:10.1016/j.jmb.2010.10.023. PMID 20974152. 
  33. ^ a b Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W (October 2010). "Atomic-level characterization of the structural dynamics of proteins". Science 330 (6002): 341–6. Bibcode:2010Sci...330..341S. doi:10.1126/science.1187409. PMID 20947758. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR001202

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The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.

Literature references

  1. Bork P, Sudol M , Trends Biochem Sci 1994;19:531-533.: The WW domain: a signalling site in dystrophin? PUBMED:7846762 EPMC:7846762

  2. Macias MJ, Hyvonen M, Baraldi E, Schultz J, Sudol M, Saraste M, Oschkinat H; , Nature 1996;382:646-649.: Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide. PUBMED:8757138 EPMC:8757138

  3. Shcherbik N, Kumar S, Haines DS; , J Cell Sci 2002;115:1041-1048.: Substrate proteolysis is inhibited by dominant-negative Nedd4 and Rsp5 mutants harboring alterations in WW domain 1. PUBMED:11870222 EPMC:11870222

  4. Kanelis V, Rotin D, Forman-Kay JD; , Nat Struct Biol 2001;8:407-412.: Solution structure of a Nedd4 WW domain-ENaC peptide complex. PUBMED:11323714 EPMC:11323714

  5. Zarrinpar A, Lim WA; , Nat Struct Biol 2000;7:611-613.: Converging on proline: the mechanism of WW domain peptide recognition. PUBMED:10932238 EPMC:10932238

  6. Bedford MT, Sarbassova D, Xu J, Leder P, Yaffe MB; , J Biol Chem 2000;275:10359-10369.: A novel pro-Arg motif recognized by WW domains. PUBMED:10744724 EPMC:10744724

  7. Lu PJ, Zhou XZ, Shen M, Lu KP; , Science 1999;283:1325-1328.: Function of WW domains as phosphoserine- or phosphothreonine-binding modules. PUBMED:10037602 EPMC:10037602

  8. Ermekova KS, Zambrano N, Linn H, Minopoli G, Gertler F, Russo T, Sudol M; , J Biol Chem 1998;272:32869-32877.: The WW domain of neural protein FE65 interacts with proline-rich motifs in Mena, the mammalian homolog of Drosophila enabled. PUBMED:9407065 EPMC:9407065

  9. Einbond A, Sudol M; , FEBS Lett 1996;384:1-8.: Towards prediction of cognate complexes between the WW domain and proline-rich ligands. PUBMED:8797792 EPMC:8797792

  10. Chen HI, Sudol M; , Proc Natl Acad Sci U S A 1995;92:7819-7823.: The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules. PUBMED:7644498 EPMC:7644498

  11. Sudol M, Chen HI, Bougeret C, Einbond A, Bork P; , FEBS Lett 1995;369:67-71.: Characterization of a novel protein-binding module--the WW domain. PUBMED:7641887 EPMC:7641887


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001202

Synonym(s): Rsp5 or WWP domain

The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [PUBMED:7846762, PUBMED:7802651, PUBMED:7828727, PUBMED:7641887]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [PUBMED:7644498, PUBMED:11911877]. It is frequently associated with other domains typical for proteins in signal transduction processes.

A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.

Gene Ontology

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Domain organisation

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Alignments

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(391)
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(2359)
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  Seed
(547)
Full
(8927)
Representative proteomes NCBI
(8316)
Meta
(391)
RP15
(1588)
RP35
(2359)
RP55
(3759)
RP75
(5200)
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  Seed
(547)
Full
(8927)
Representative proteomes NCBI
(8316)
Meta
(391)
RP15
(1588)
RP35
(2359)
RP55
(3759)
RP75
(5200)
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: WW_rsp5_WWP;
Type: Domain
Author: Finn RD
Number in seed: 547
Number in full: 8927
Average length of the domain: 30.00 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 6.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.9 21.9
Trusted cut-off 21.9 21.9
Noise cut-off 21.8 21.8
Model length: 31
Family (HMM) version: 21
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Species distribution

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Interactions

There are 3 interactions for this family. More...

EF-hand_2 WW Rotamase

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the WW domain has been found. There are 119 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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