title: WW domains provide a platform for the assembly of multiprotein networks.
abstract: WW domains are protein modules that mediate protein-protein interactions through recognition of proline-rich peptide motifs and phosphorylated serine/threonine-proline sites. To pursue the functional properties of WW domains, we employed mass spectrometry to identify 148 proteins that associate with 10 human WW domains. Many of these proteins represent novel WW domain-binding partners and are components of multiprotein complexes involved in molecular processes, such as transcription, RNA processing, and cytoskeletal regulation. We validated one complex in detail, showing that WW domains of the AIP4 E3 protein-ubiquitin ligase bind directly to a PPXY motif in the p68 subunit of pre-mRNA cleavage and polyadenylation factor Im in a manner that promotes p68 ubiquitylation. The tested WW domains fall into three broad groups on the basis of hierarchical clustering with respect to their associated proteins; each such cluster of bound proteins displayed a distinct set of WW domain-binding motifs. We also found that separate WW domains from the same protein or closely related proteins can have different specificities for protein ligands and also demonstrated that a single polypeptide can bind multiple classes of WW domains through separate proline-rich motifs. These data suggest that WW domains provide a versatile platform to link individual proteins into physiologically important networks.
authors.affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Ingham
authors.forename: Karen
authors.initials: K
authors.lastname: Colwill
authors.forename: Caley
authors.initials: C
authors.lastname: Howard
authors.forename: Sabine
authors.initials: S
authors.lastname: Dettwiler
authors.forename: Caesar S H
authors.initials: CS
authors.lastname: Lim
authors.forename: Joanna
authors.initials: J
authors.lastname: Yu
authors.forename: Kadija
authors.initials: K
authors.lastname: Hersi
authors.forename: Judith
authors.initials: J
authors.lastname: Raaijmakers
authors.forename: Gerald
authors.initials: G
authors.lastname: Gish
authors.forename: Geraldine
authors.initials: G
authors.lastname: Mbamalu
authors.forename: Lorne
authors.initials: L
authors.lastname: Taylor
authors.forename: Benny
authors.initials: B
authors.lastname: Yeung
authors.forename: Galina
authors.initials: G
authors.lastname: Vassilovski
authors.forename: Manish
authors.initials: M
authors.lastname: Amin
authors.forename: Fu
authors.initials: F
authors.lastname: Chen
authors.forename: Liudmila
authors.initials: L
authors.lastname: Matskova
authors.forename: Gösta
authors.initials: G
authors.lastname: Winberg
authors.forename: Ingemar
authors.initials: I
authors.lastname: Ernberg
authors.forename: Rune
authors.initials: R
authors.lastname: Linding
authors.forename: Paul
authors.initials: P
authors.lastname: O'donnell
authors.forename: Andrei
authors.initials: A
authors.lastname: Starostine
authors.forename: Walter
authors.initials: W
authors.lastname: Keller
authors.forename: Pavel
authors.initials: P
authors.lastname: Metalnikov
authors.forename: Chris
authors.initials: C
authors.lastname: Stark
authors.forename: Tony
authors.initials: T
authors.lastname: Pawson
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry; D002853:Chromatography, Liquid; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000378:metabolism; D030562:Databases, Protein; D004591:Electrophoresis, Polyacrylamide Gel; D005982:Glutathione Transferase / Q000378:metabolism; D006801:Humans; D019169:Jurkat Cells; D008024:Ligands; D013058:Mass Spectrometry; D008954:Models, Biological; D008969:Molecular Sequence Data; D046912:Multiprotein Complexes / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D010766:Phosphorylation; D010802:Phylogeny; D011392:Proline / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012326:RNA Splicing; D012333:RNA, Messenger / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000737:chemistry; D014158:Transcription, Genetic; D014357:Trypsin / Q000494:pharmacology; D025801:Ubiquitin / Q000737:chemistry; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry
chemical_list: D002843:Chromatin; D018076:DNA, Complementary; D008024:Ligands; D046912:Multiprotein Complexes; D010455:Peptides; D012333:RNA, Messenger; D011993:Recombinant Fusion Proteins; D025801:Ubiquitin; D011392:Proline; D044767:Ubiquitin-Protein Ligases; D005982:Glutathione Transferase; D014357:Trypsin