Structure of FBP11 WW1-PL Ligand Complex Reveals the Mechanism of Proline-rich Ligand Recognition by Group II/III WW Domains

Abstract

FBP11/HYPA is a mammalian homologue of yeast splicing factor Prp40. The first WW domain of FBP11/HYPA (FBP11 WW1) is essential for preventing severe neurological diseases such as Huntington disease and Rett syndrome and strongly resembles the WW domain of FCA, the essential regulator for flowering time control. We have solved the structure of FBP11 WW1 and a Pro-Pro-Leu-Pro ligand complex, and demonstrated the binding mechanism with mutational analysis using surface plasmon resonance. The overall structure of FBP11 WW1 in the complex form is quite similar to the structures of WW domains from Group I and IV in complexes. In addition, conformation of FBP11 WW1 does not change much upon ligand binding. The binding orientation of the ligand against FBP11 WW1 is the same as that of the Group IV WW domainligand complex, but opposite to that of the Group I complex. The ligand interacts with two grooves formed by surface aromatic residues. The Pro and Leu residues in the ligand interact with the grooves and the Loop I region of FBP11 WW1, respectively, which are necessary interactions for binding the ligand. Interestingly, the two aromatic grooves recognize the Pro residues in entirely different manners, which allows FBP11 WW1 to recognize shorter sequences than the SH3 domain. Combined with homology models of other WW domains, the present report shows the detailed mechanism of ligand binding by Group II/III WW domains, and provides information useful in designing drugs to treat neurodegenerative diseases. FBP112 /HYPA is a mammalian homologue of yeast splicing factor Prp40 and acts to enhance the efficiency of splicing in mammalian cells (1). WW domains of FBP11/HYPA and its related proteins bind to huntingtin, the protein responsible for Huntington disease (2, 3). In addition, a loss of binding of these WW domains to methyl-CpG-binding protein MeCP2 leads to symptoms of Rett syndrome (4). Thus, WW domains of FBP11 are directly involved in development of these severe neurological disorders.FBP11/HYPA has two WW domains that bind to prolinerich ligands, including those with the -Pro-Pro-Leu-Prosequence, the PL motif (5). The first WW domain of FBP11/ HYPA is highly similar to the FCA WW domain (FCA WW), which binds to a PL motif of FY in Arabidopsis thaliana (6). Interaction between FCA and FY is essential to a pathway regulating the flowering transition in A. thaliana.The WW domain is a well known protein module that mediates protein-to-protein interactions by binding to proline-containing ligands. Recent structural studies have revealed that WW domains have a -Xaa-Pro-binding groove (XP groove) that recognizes proline residues (7, 8). The aromatic residues, Trp and Tyr, form the groove.Originally, the PL and PR motifs were proposed as the ligands specific to Group II and III WW domains, respectively (5, 9). More recently, several studies have shown that many Group II and III WW domains have common ligand specificity, leading to the new definition of one larger group referred to as Group II/III, which was formed by mer...

Structure and Function of the Two Tandem WW Domains of the Pre-mRNA Splicing Factor FBP21 (Formin-binding Protein 21)

“…Our results show that the two WW domains of FBP21 both recognize peptides containing PPR, PPLP, as well as PPPP motifs. We also found that the binding interfaces on both WW domains involve both the XP and XP2 grooves, similar to what has been reported for group II domains (49,50). In conclusion, WW domains of group II and group III cannot be clearly differentiated based on their three-dimensional structure, binding interface, and ligand specificity and should be viewed as a single group.…”

Interaction with Polyglutamine-expanded Huntingtin Alters Cellular Distribution and RNA Processing of Huntingtin Yeast Two-hybrid Protein A (HYPA)

“…The bipartite mode of the PP1 and PP3 moieties in Htt-PRR and the tandem WW domains in HYPA significantly enhance their binding affinity. The first WW domain of HYPA is well ordered (29,(35)(36)(37), whereas it may have a chaperoning effect on the folding of the secondary WW domain. Our results indicate that the two WW domains work as a unit to interact with Htt-PRR.…”

Structural Basis for Polyproline Recognition by the FE65 WW Domain

“…28,29 By contrast, group II and III WW domains have an additional groove, XP2, which is formed by the conserved tyrosine and an aromatic residue in β2 strand. 33,34 In this respect, groups II and III are more similar to SH3 domains, which have two successive XP grooves, suggesting that these structurally and evolutionary unrelated protein modules have converged on a similar mechanism for polyproline recognition. Based on the distinct structural features and similar binding specificities of group II and III WW domains, including recognition of uninterrupted polyproline sequences (PPPPP) in addition to PL and PR motifs, it was recently proposed that these groups be merged into a larger class II/III.…”