WW domains provide a platform for the assembly of multiprotein networks.
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.
Ingham
Robert J
RJ
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Colwill
Karen
K
Howard
Caley
C
Dettwiler
Sabine
S
Lim
Caesar S H
CS
Yu
Joanna
J
Hersi
Kadija
K
Raaijmakers
Judith
J
Gish
Gerald
G
Mbamalu
Geraldine
G
Taylor
Lorne
L
Yeung
Benny
B
Vassilovski
Galina
G
Amin
Manish
M
Chen
Fu
F
Matskova
Liudmila
L
Winberg
Gösta
G
Ernberg
Ingemar
I
Linding
Rune
R
O'donnell
Paul
P
Starostine
Andrei
A
Keller
Walter
W
Metalnikov
Pavel
P
Stark
Chris
C
Pawson
Tony
T
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
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