Common Mechanism of Ligand Recognition by Group II/III WW Domains

Abstract

WW domain is a well known protein module that mediates protein to protein interactions by binding to proline-containing ligands. Based on the ligand predilections, the WW domains have been classified into four major groups. Group II and III WW domains have been reported to bind the proline-leucine and proline-arginine motifs, respectively. In the present study, using surface plasmon resonance technique we have shown that these WW domains have almost indistinguishable ligand preferences and kinetic properties. Hence, we propose that Group II and III WW domains should be joined together as one group (Group II/III). Unlike Group I and IV WW domains, Group II/III WW domains can bind simple polyprolines as well as the proline-leucine and proline-arginine motifs, and they possess two Xaa-proline (where Xaa is any amino acid) binding grooves similar to SH3 domains. Our work assigns Group II and III WW domains to a larger family of polyproline-binding modules and proteins, which includes SH3 domains and profilin. Because polyprolines belong to the most frequently found peptide motifs in several genomes, our study implies the versatile importance of Group II/III WW domains in signaling. WW domain is a well known protein module that mediates protein to protein interactions by binding to proline-containing ligands. Based on the ligand predilections, the WW domains have been classified into four major groups. Group II and III WW domains have been reported to bind the proline-leucine and proline-arginine motifs, respectively. In the present study, using surface plasmon resonance technique we have shown that these WW domains have almost indistinguishable ligand preferences and kinetic properties. Hence, we propose that Group II and III WW domains should be joined together as one group (Group II/III). Unlike Group I and IV WW domains, Group II/III WW domains can bind simple polyprolines as well as the proline-leucine and proline-arginine motifs, and they possess two Xaa-proline (where Xaa is any amino acid) binding grooves similar to SH3 domains. Our work assigns Group II and III WW domains to a larger family of polyproline-binding modules and proteins, which includes SH3 domains and profilin. Because polyprolines belong to the most frequently found peptide motifs in several genomes, our study implies the versatile importance of Group II/III WW domains in signaling. The WW domain is composed of 30–40 amino acids and named after two tryptophan (W) residues that are highly conserved and spaced 20–22 amino acids apart (1Bork P. Sudol M. Trends Biochem. Sci. 1994; 19: 531-533Google Scholar, 2Sudol M. Hunter T. Cell. 2000; 103: 1001-1004Google Scholar). The domain binds proline-rich or proline-containing ligands (3Chen H.I. Sudol M. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 7819-7823Google Scholar, 4Chan D.C. Bedford M.T. Leder P. EMBO J. 1996; 15: 1045-1054Google Scholar, 5Lu P.J. Zhou X.Z. Shen M. Lu K.P. Science. 1999; 283: 1325-1328Google Scholar). WW domain-containing proteins have been shown to be involved in a variety of cellular processes including cell cycle control (Pin1/Ess1), ubiquitin ligation (Nedd4/Rsp5 and smurf1), and coactivation of transcription (YAP65) (reviewed in Refs. 2Sudol M. Hunter T. Cell. 2000; 103: 1001-1004Google Scholar and 6Kay B.K. Williamson M.P. Sudol M. FASEB J. 2000; 14: 231-241Scopus (1026) Google Scholar). A few WW domain-containing proteins have been implicated, either directly or indirectly, in a variety of human diseases such as Liddle's syndrome of hypertension, Duchenne and Becker muscular dystrophies, Huntington's disease, and Alzheimer's disease (7Faber P.W. Barnes G.T. Srinidhi J. Chen J. Gusella J.F. MacDonald M.E. Hum. Mol. Genet. 1998; 7: 1463-1474Google Scholar, 8Huang X. Poy F. Zhang R. Joachimiak A. Sudol M. Eck M.J. Nat. Struct. Biol. 2000; 7: 634-638Google Scholar, 9Sudol M. Sliwa K. Russo T. FEBS Lett. 2001; 490: 190-195Google Scholar). FBP11, a mammalian homologue of yeast Prp40, binds the Pro-Leu (PL) motif (4Chan D.C. Bedford M.T. Leder P. EMBO J. 1996; 15: 1045-1054Google Scholar). FBP11 and WAC act as a component of the splicing factor (10Bedford M.T. Reed R. Leder P. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 10602-10607Google Scholar, 11Xu G.M. Arnaout M.A. Genomics. 2002; 79: 87-94Google Scholar). FBP11, HYPB, and HYPC also bind Huntingtin, a protein responsible for Huntington's disease (7Faber P.W. Barnes G.T. Srinidhi J. Chen J. Gusella J.F. MacDonald M.E. Hum. Mol. Genet. 1998; 7: 1463-1474Google Scholar). Fe65 binds β-amyloid precursor protein, a precursor of β-amyloid peptide, which constitutes the extracellular neuritic plaques in Alzheimer disease (9Sudol M. Sliwa K. Russo T. FEBS Lett. 2001; 490: 190-195Google Scholar, 12Selkoe D.J. Science. 1997; 275: 630-631Google Scholar). The WW domain of Fe65 binds the proline-rich region of Mena, a mammalian homologue of Drosophila melanogaster Ena, which has been identified in a specific screen for dominant mutations that alleviate the Abl phenotype (13Gertler F.B. Doctor J.S. Hoffmann F.M. Science. 1990; 248: 857-860Google Scholar, 14Ermekova K.S. Zambrano N. Linn H. Minopoli G. Gertler F. Russo T. Sudol M. J. Biol. Chem. 1997; 272: 32869-32877Google Scholar). Fe65 and β-amyloid precursor protein are involved in the reconstruction of actin cytoskeleton, which suggests the concerted action of these proteins with Mena and/or Abl (9Sudol M. Sliwa K. Russo T. FEBS Lett. 2001; 490: 190-195Google Scholar, 15Sabo S.L. Ikin A.F. Buxbaum J.D. Greengard P. J. Cell Biol. 2001; 153: 1403-1414Google Scholar). The WW domain of FBP30 has been reported to bind the Pro-Arg (PR) motif (10Bedford M.T. Reed R. Leder P. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 10602-10607Google Scholar, 16Bedford M.T. Sarbassova D. Xu J. Leder P. Yaffe M.B. J. Biol. Chem. 2000; 275: 10359-10396Google Scholar). WW domains have been classified into four groups according to their ligand specificity: Group I recognizes Pro-Pro-Xaa-Tyr (PY motif); Group II recognizes Pro-Pro-Leu-Pro (PL motif); Group III recognizes proline-rich segments with Arg residues (PR motif); and Group IV recognizes Ser(P)/Thr(P)-Pro-(pS/pT-P motif) (2Sudol M. Hunter T. Cell. 2000; 103: 1001-1004Google Scholar, 9Sudol M. Sliwa K. Russo T. FEBS Lett. 2001; 490: 190-195Google Scholar). According to this classification, the WW domains of FBP11 and Fe65 have been assigned to Group II, whereas that of FBP30 has been assigned to Group III. The crystal structures of the Group I and IV WW domains complexed with their ligands have revealed a common structural basis to recognize the Pro-containing ligands; the XP groove, which is formed by two aromatic rings with nearly parallel alignment, plays a pivotal role in recognizing the Xaa-Pro segment in the ligands (17Zarrinpar A. Lim W.A. Nat. Struct. Biol. 2000; 7: 611-613Google Scholar, 18Macias M.J. S. Sudol M. FEBS Lett. 2002; Scholar, A. Lim W.A. Scholar). In Group I and IV WW domains have been shown to possess their ligand the and the which to the specific ligand M. K. K. M. J. Biol. Chem. 2002; Scholar). the the Group II and III WW domains has been the WW domain of Fe65 has been classified as Group II in one K.S. Zambrano N. Linn H. Minopoli G. Gertler F. Russo T. Sudol M. J. Biol. Chem. 1997; 272: 32869-32877Google as Group III in M.T. Sarbassova D. Xu J. Leder P. Yaffe M.B. J. Biol. Chem. 2000; 275: 10359-10396Google Scholar). In are a few ligand motifs that can also bind of the WW domains in these the motif and polyprolines (7Faber P.W. Barnes G.T. Srinidhi J. Chen J. Gusella J.F. MacDonald M.E. Hum. Mol. Genet. 1998; 7: 1463-1474Google Scholar, M.T. Reed R. Leder P. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 10602-10607Google Scholar, A. M. S. J. Biol. Chem. 1999; Scholar, M.T. A. Yaffe M.B. S. Leder P. S. J. Biol. Chem. 2000; 275: Scholar). the of the Group II and III WW domains in we have binding using surface plasmon resonance surface plasmon surface plasmon also binding by of the WW domain H. J. Zhang D. S. J. M. Chen M. R. Sudol Scholar). found that the WW domains classified as II and III similar ligand and that they to bind ligands. propose that the Group II and III WW domains should be classified into one Group we have and revealed that the Group II and III WW domains have a that is formed by two aromatic rings with nearly parallel alignment, similar to the XP groove, on the The importance of this XP we named to recognize their ligands by Our of WW domains and for the this the WW domains of human and and by a in which several as the for the The the WW domain of human and the WW domain of FBP30 by using their as which by H. and M. T. Bedford M.T. Sarbassova D. Xu J. Leder P. Yaffe M.B. J. Biol. Chem. 2000; 275: 10359-10396Google Scholar, H. T. Biochem. 1999; Scholar). The the and of the The for proteins of the WW domain of and the WW domain of human by J. Shen R. K. Sudol M. Shen J. Biol. Chem. 1997; 272: Scholar). The for protein of the WW domain of FBP11 by M. T. Bedford M.T. D.C. Leder P. EMBO J. 1997; Scholar). The WW domains of HYPB, and Fe65 into as by H. J. Zhang D. S. J. M. Chen M. R. Sudol Scholar). and the WW domains in or and with The by for the The WW domains and by with a with a of in by on a The in the as H. J. Zhang D. S. J. M. Chen M. R. Sudol Scholar). of human WW domains on and proline-rich the human to the of and as H. J. Zhang D. S. J. M. Chen M. R. Sudol Scholar). for the ligand by peptide on a and acids with and and respectively. the and in in the of and by with a by on a The amino of the ligand peptide the peptide the in the present peptide the peptide the and peptide the using a ligand peptide on a cell of a by the with a peptide in of a peptide in the The with The binding using the WW domains as in and The with The of the WW domains on the of the protein The by M.A. Zhou M. J. J. Biol. Chem. 1994; Scholar, M. K. A. H. FEBS Lett. 1999; Scholar). the of a cell ligand peptide the of the the the and is the of the to the A to the for the by The and and the using using N. 1997; and The crystal structures of and and the structures of and as the for the WW domains of and and and using R. M. K. J. Mol. 1996; 14: Scholar). The to the N. 1997; Scholar). binding by to the ligand of several WW domains to of and are shown in A and The ligands and which the and motifs and are the ligands for Group II, and IV WW domains, respectively. In in the present WW domains as binding the WW domains of and classified as Group of and Group that of Group and of and Group M. K. K. M. J. Biol. Chem. 2002; Scholar). The WW domains of WAC and have been classified of the WW domains in the present in the of the The proteins have the to of the of the the of in the of the proteins we in the present study and the the of WW as Group proteins have WW domains. In our we WW domains such domain The WW domain of the WW domain of and the WW domain of most with the peptide that a the for the Group I with of are in with the for Group I WW domains using including M.J. M. J. Sudol M. M. H. 1996; Scholar, H. K.S. S. B.K. Sudol M. Biol. Chem. 1997; Scholar). these the of well in the present The WW domains of and also to the peptide that a a for the Group II ligands. their to the peptide and in to the that the WW domains of and highly to the the Group I of the Group I WW domains to of WW as Group binding to the peptide shown for the WW domains of HYPB, and the and motifs similar binding to WW domains. a in binding common for Group II WW domains. the WW domain of (Group that the most ligand the peptide, the The and peptide motif) also to with and larger the The WW domain of WAC to possess the Group II to the peptide most In binding to the Group II and III ligands with most larger the with the WAC WW the WW domains of HYPB, and most to in our The WW domains of Fe65 and also to the and motif most with and larger to the peptide, respectively. the the WW domain of to the peptide, to which and to the and motifs, respectively. is that the WW domain of to the and motifs with similar The similar binding to the and motifs also in the Group II WW domains and reported the of most The group of Fe65 in the present Our that Fe65 the peptide, the Group II also to the the Group III with the of should the peptide as one of the ligand motifs for the WW domains of HYPB, and binding to to the of WW as Group WW domain of a Group III WW most to the the Group III and to the and motifs, the Group II to a to the and peptide with and larger to the also found that to the motif a Group II WW Our on the Group II and III WW domains that Group II and III WW domains their the and motifs, and that in their ligand preferences are similar or almost of WW as Group is that the Group IV WW domains bind to the The WW domains of and classified as Group IV (2Sudol M. Hunter T. Cell. 2000; 103: 1001-1004Google Scholar, 5Lu P.J. Zhou X.Z. Shen M. Lu K.P. Science. 1999; 283: 1325-1328Google Scholar, M. K. K. M. J. Biol. Chem. 2002; Scholar). In the present study we that WW domain of and most to the the and proteins The WW domain of with the peptide, a Group III with a of with the the of the Group IV WW domains highly specific to the Group IV ligands. should be that of the Group IV WW domains to the of WW as Group II or kinetic of the Group II and III the the the II and III WW domains common in of the of ligand also in the binding The kinetic of ligand binding for WW domains II and III of these WW domains a common in the for and WW domains with the motif with the and the motifs and the motif the and is that the WW domain of with the motif with the of of be one of the of to the also the for the WW domains and the common ligand of the Group II and III WW domains. we can that domains have of binding ligands the of the Group The of binding ligands in Group I is in the of whereas the of binding ligands the and motifs are in the of and I and these WW domains the motif the and motifs and the motif is that these WW domains the Group II and Group III motifs to a similar The that the in ligand of these WW domains is almost are with the the as binding of WW domains groups of Pro-containing ligands The binding of WW domains HYPB, and are as the of ligands that a domain binds to in four The of ligands the domain is also The and to these are as H. J. Zhang D. S. J. M. Chen M. R. Sudol Scholar). The ligands in this by human protein with the a ligand is by the to a protein and on of amino acids to the and of the protein as The ligand is amino The to a ligand into a group are for the or motif) to be amino acids either of a The of ligands in this are in The in the motifs are in the The domain and are of in a of of ligands motif for motif motif motif motif in a The proteins of the WW domains in this the of the WW domains and as in of the of WW of our to of WW domains in of structural common for Group II and III WW domains. I and IV WW domains the of their to recognize their ligands that the WW domains classified as II and III also the to recognize their ligands. of the Group II and III WW domains and on the and their with of Group I and IV WW domains to the structural basis of their ligand have the common for residues of WW domains to the of WW domains the for Group I and IV WW domains, the XP also found on the of the WW domains of and is formed by highly conserved aromatic and and is for ligand by Group II and III WW domains, of their ligands Xaa-Pro segments the of the groove, of WW domains into and the ligand of the WW domains of groups. The of Group I and IV have been M. K. K. M. J. Biol. Chem. 2002; Scholar). In to the WW domains the XP formed by and of the WW domains classified with the shown in A. A common on the of in the present The the of WW domains on the structures The are to whereas the are to and The ligand are in the human the domains that in the present Group I and IV WW domains have the and the which their ligand X. Poy F. Zhang R. Joachimiak A. Sudol M. Eck M.J. Nat. Struct. Biol. 2000; 7: 634-638Google Scholar, M. K. K. M. J. Biol. Chem. 2002; Scholar, D. J.D. Nat. Struct. Biol. 2001; Scholar). The in Group I WW domains is formed by and and is for of the in the motif of the ligand of the WW domains of or can the they have The in Group IV WW domains is formed by and and is for of the group in the motif of the WW domains or WW domains a they of the or a is that Group II and III WW domains have a similar ligand surface their and in ligand have been shown to be The structures of Group II and III WW domains common structural the ligand a formed by two aromatic rings and and in I The two aromatic and a that the XP the importance of these we and the and the in the found that the of the WW domain a for of the Group II and III ligands to the motif the the of the WW domain of which to Group the to bind to the motif X. Sudol M. J. Biol. Chem. 1999; Scholar). The of this binding which larger that of the WW domain of and the importance of for Group II and III WW domains to recognize their the the and mutations in the WW domain of the ligand binding the on I is for the ligand binding of Group II and III WW domains. Group II and III WW domains recognize their ligands and by the XP and the similar Because the ligands of Group II and III WW domains possess two or Xaa-Pro we propose that the XP formed by and recognizes a Xaa-Pro segment in a this the residues and as the the XP binding and that several WW domains of Group II or III assigned to either of the two groups of ligand by we to the that II and III WW domains one larger that also with SH3 domains. to the binding the of the of WW domains H. J. Zhang D. S. J. M. Chen M. R. Sudol of WW domain Our is that the of WW domains that assigned to either Group II or III WW domains belong to one group of domains with a binding that is similar to that of SH3 domains. reported that the WW domains of and to the motif and the and they have been classified as II and M.T. Sarbassova D. Xu J. Leder P. Yaffe M.B. J. Biol. Chem. 2000; 275: 10359-10396Google Scholar, M.T. A. Yaffe M.B. S. Leder P. S. J. Biol. Chem. 2000; 275: Scholar, M.T. D.C. Leder P. EMBO J. 1997; Scholar). we have shown by binding that the WW domains of HYPB, and are to bind the and motifs as well as simple with to that their ligand preferences should be as of the WW domains have similar kinetic with to ligand and Our in of the the and Sudol on the WW domains of Group II and III and the of their binding with of SH3 domains M.J. S. Sudol M. FEBS Lett. 2002; Scholar). Group II and III WW domains the with the domains M. K. A. H. FEBS Lett. 1999; Scholar, M. S. R. H. K. T. K. T. J. Biol. Chem. 1996; Scholar, FEBS Lett. 1999; Scholar). the Group II and III WW domains which in domains and in the of proteins into a binding of WW domains with the domains of The as a of Group II and III WW that the Group II and III WW domains have the as the for their specific ligand The structural of the XP and grooves suggests that the is also involved in the of Xaa-Pro segment in the Group II and III ligands. Our the importance of and the for ligand binding by the Group II and III WW domains. the to be the structural R. Bedford M.T. G. M. T. M.A. R. M. Sudol M. U. FEBS Lett. 2002; Scholar for of the Group II and III WW domains for their ligand Group IV WW domains also have a that the of the two highly conserved aromatic residues and and Group II and III WW domains, they are to bind the or In the crystal of a Group IV WW domain complexed with ligand M.A. M.E. Lu K.P. Hunter T. Nat. Struct. Biol. 2000; 7: the aromatic of is parallel with is nearly to the aromatic of the two aromatic rings of and in Group IV WW domains a for of the Xaa-Pro of WW and have the similar of Group II and III WW domains with to their and propose that the WW domains classified into two II and should be classified into a group Group The for the of WW domains are shown in is the (2Sudol M. Hunter T. Cell. 2000; 103: 1001-1004Google Scholar, 9Sudol M. Sliwa K. Russo T. FEBS Lett. 2001; 490: 190-195Google Scholar). The Group II/III WW domains bind the and motifs, of which have two or Xaa-Pro The two Xaa-Pro segments are by the two Xaa-Pro binding grooves XP and formed by aromatic rings with nearly parallel and The ligand of WW domains can be on the shown in have classified the WW domains on the and have the ligand for WW and WW domains the to be classified as and whereas the WW domains of for Group II/III WW that should the II a the rings of in 1998; Scholar). In the SH3 domains and bind the proline-rich the H. Chen S. D.C. S.L. Cell. 1994; Scholar, Nat. Struct. Biol. 1997; Scholar). the Group II/III WW domains are to bind the ligands that the Xaa-Pro segment and in the the XP groove, the Xaa-Pro segment and should the and The two XP grooves the formed by the aromatic rings of and can well to the and grooves of the According to this a ligand for Group II/III WW domains should be residues whereas residues to bind 1996; Scholar). In the WW domain of a Group II/III WW has been reported to bind X. Sudol M. J. Biol. Chem. 1999; Scholar). A be to bind in the according to our has the of In a can bind and SH3 domains in two W.A. F.M. 1994; Scholar, Nat. Struct. Biol. 1999; Scholar). of the Group II/III WW domains have been reported to bind the and motifs (10Bedford M.T. Reed R. Leder P. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 10602-10607Google Scholar, A. M. S. J. Biol. Chem. 1999; Scholar). the of the motifs that can bind Group II/III WW domains, the is The and segments that should bind the two XP grooves on the surface of Group II/III WW domains. is that the XP grooves can recognize Xaa-Pro The XP of SH3 domains binds Xaa-Pro the has a formed by a and a (17Zarrinpar A. Lim W.A. Nat. Struct. Biol. 2000; 7: 611-613Google Scholar, A. Lim W.A. Scholar, Lim W.A. Science. 1998; Scholar). is that the residues and which are the residues of the XP segments on should be The specific of the two XP grooves for recognizing the Xaa-Pro is most responsible for the and binding of the Group II/III WW domains. the XP to the formed by the SH3 and WW domains and their ligands (17Zarrinpar A. Lim W.A. Nat. Struct. Biol. 2000; 7: 611-613Google Scholar). and almost of XP grooves is to the of specific protein that cellular with the SH3 in of and SH3 domains have two XP binding a similar to the Group II/III WW domains (17Zarrinpar A. Lim W.A. Nat. Struct. Biol. 2000; 7: 611-613Google Scholar, A. Lim W.A. whereas the Group I and IV WW domains have one XP binding the ligand by Group II/III WW domains be similar to that by the SH3 domains to that by Group I and IV WW domains M.J. S. Sudol M. FEBS Lett. 2002; Scholar). The of the ligands for SH3 domains in which the two residues by two residues a role in the The of the is also found in the of the ligands for Group II/III WW domains. SH3 domains also Arg or in their ligand for the of the Arg the by H. Chen S. D.C. S.L. Cell. 1994; Scholar, S. Chen H. S.L. Science. 1994; Scholar). In Group II/III WW domains Arg in the as revealed by our and as well as by of Arg residues M.T. A. Yaffe M.B. S. Leder P. S. J. Biol. Chem. 2000; 275: Scholar). The of Arg residues in the binding the SH3 domains of and whereas the binding to WW domain of is The two XP grooves in the Group II/III WW domains are to in the SH3 domains, which the binding of the Group II/III WW domains to the motif that of the SH3 domains. Group II/III WW domains and SH3 domains for the ligands in the of their ligands are common to M.J. S. Sudol M. FEBS Lett. 2002; Scholar, M.T. A. Yaffe M.B. S. Leder P. S. J. Biol. Chem. 2000; 275: Scholar). of Group II/III WW and the in WW domain of Fe65 has been reported to bind to the motif of Mena, a protein involved in reconstruction K.S. Zambrano N. Linn H. Minopoli G. Gertler F. Russo T. Sudol M. J. Biol. Chem. 1997; 272: 32869-32877Google Scholar, 15Sabo S.L. Ikin A.F. Buxbaum J.D. Greengard P. J. Cell Biol. 2001; 153: 1403-1414Google Scholar). Mena the also Our the binding that the Fe65 and Mena is by the the the FBP11, HYPB, and HYPC have been reported to bind (7Faber P.W. Barnes G.T. Srinidhi J. Chen J. Gusella J.F. MacDonald M.E. Hum. Mol. Genet. 1998; 7: 1463-1474Google Scholar). the motif the the motif should act as motif in is one of the most frequently found motifs in the of and yeast G.M. M.E. P.W. R. S. M.P. S. M. T. P. D. A. A. F. P. J. Zhang J. S. Science. 2000; Scholar). In a of proteins are known to in cell and major cellular and processes In the present study, we have shown that the Group II/III WW domains are to bind simple the Group I and IV WW domains. have found Group II/III WW domains of WW domains in a that of WW domains in the of simple the as well as the and work the structural and of Group II/III WW domains and their importance in by H. for the of J. Shen for the of and and M. T. Bedford for the of and the of