WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains

Otte, Livia; Wiedemann, Urs Achim; Schlegel, Brigitte; Pires, Juliana Rico; Beyermann, Michael; Schmieder, Peter; Krause, Gerd; Volkmer, Rudolf; Schneider‐Mergener, Jens; Oschkinat, Hartmut

doi:10.1110/ps.0233203

Cited by 123 publications

(156 citation statements)

References 29 publications

Supporting

Mentioning

140

Contrasting

Unclassified

Order By: Relevance

“…A diverse set of PRS from various proteins was probed by the GST variants of both domains and revealed a striking resemblance in their interaction profile (Fig. 4A and supplemental Table S5) in agreement with published recognition motifs (13,39). In spliceosomal PRS hubs, binding sites of the two PRDs are frequently overlapping, and in the (44).…”

Section: Table I Proteins Found In the Pulldown Experiments Compared supporting

confidence: 72%

Proline-rich Sequence Recognition

Kofler

Schuemann

Merz

et al. 2009

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

The two catalytic steps of splicing are a conceptually simple process that results in the RNA-mediated excision of introns (1). Complexity arises at the level of RNA-RNA and protein-RNA interactions that are needed for the correct spatial positioning of the critical bases, unwinding of RNA, and coupling of splicing to other processes as for example transcription (2, 3), nonsense-mediated mRNA decay (4), or mRNA transport (5, 6). Pre-mRNA splicing is catalyzed by the spliceosome, a dynamic macromolecular machine, which consists of the small nuclear ribonuclear particles (snRNPs), 1 U1, U2, U4/U6, and U5, and numerous non-snRNP proteins (7). The snRNPs interact with the intron in an ordered manner. First the U1 snRNP binds to the 5Ј splice site, whereas the U2 snRNP stably associates with the branch site forming complex A. Subsequently the tri-snRNP U4/U6.U5 is stably integrated to form complex B. This complex undergoes large structural rearrangements that lead to the formation of the activated spliceosomal complex B*. The catalytic steps of the transesterification then occur in complex C. Proline-rich sequences (PRS) are frequently found in spliceosomal proteins, and they are mostly assigned to unstructured regions of the corresponding full-length proteins (8). They serve as docking sites for so-called proline-rich sequence recognition domains (PRDs), and their interactions are characterized by low affinities and moderate specificities (9 -13). Several of the interactions between PRD and their proline-rich binding sites within the spliceosome have been characterized in vitro in great detail, but little is known about their functional importance. One interesting spliceosomal protein that mediates PRS interactions is CD2BP2/52K (14). It is a component of the U5 snRNP (15, 16) and contains a GYF adaptor domain that recognizes PRS via a set of conserved aromatic amino acids (17)(18)(19). A likely interaction partner of the GYF domain is the core splicing protein SmB/BЈ, which is present in all snRNPs. The GYF domain of CD2BP2/52K comprises a second interaction surface on a site opposite to the PRS binding epitope. This site is bound by the essential splicing protein U5-15K (16, 20). Considering that the U5 snRNP protein Prp6 interacts with the N-terminal part of CD2BP2/52K (16), several independent interactions seemingly contribute to the association of the protein with the U5 snRNP. However, for the GYF domain we could identify by phage display and peptide SPOT analysis additional interaction sites in other proteins suggesting that further "moonlighting" functions of the GYF domain might exist (21,22). This has set the basis for the current study where we performed pulldown experiments to define more generally the importance of CD2BP2/52K-GYF for the assembly of protein complexes. Utilizing the GYF domain fused to GST as bait, a large number of protein components of the U1, U2, U5, and the U4/U6.U5 tri-snRNP were co-precipitated. The association of most proteins was highly dependent on the PRS binding site in the GY...

show abstract

Section: Table I Proteins Found In the Pulldown Experiments Compared supporting

confidence: 72%

Proline-rich Sequence Recognition

Kofler

Schuemann

Merz

et al. 2009

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

show abstract

“…The fact that neither p53 nor JNK was identified in our experiments may indicate that the cDNA clones encoding these proteins are not represented in the high-density protein array. It is worth noting, however, that the p53 proline-rich region does not contain any PPXY motifs, and it has been well documented that ligand preference by the various known WW domains is 'highly specific' (Kay et al, 2000;Sudol and Hunter, 2000;Kasanov et al, 2001;Otte et al, 2003). Indeed, we have presented evidence that the WWOX WW domain specifically binds the PPXY motif.…”

Section: Discussionmentioning

confidence: 58%

WWOX binds the specific proline-rich ligand PPXY: identification of candidate interacting proteins

et al. 2004

View full text Add to dashboard Cite

WWOX, the gene that maps to common chromosomal fragile site FRA16D, is frequently affected by aberrations in multiple types of cancers. WWOX encodes a 46 kDa protein that contains two WW domains and a short-chain oxidoreductase (SDR) domain. We recently demonstrated that ectopic expression of WWOX inhibits xenograft tumor growth of tumorigenic breast cancer cells. Little is known of the biochemical function(s) of WWOX. The SDR domain is predicted to be involved in sex-steroid metabolism and the WW domains are likely involved in protein-protein interactions. In this report, we identify the specific proline-rich ligand for WWOX as PPXY and show that the amino-terminal WW domain is responsible for this interaction. Using the WWOX WW domains as a probe, we screened high-density protein arrays and identified five candidate-binding partners. The binding to one of these candidates, small membrane protein of the lysosome/late endosome (SIMPLE), was further analysed, and we observed that a specific PPSY motif in the SIMPLE amino-acid sequence was required to interact with the amino-terminal WW domain of WWOX. In addition, immunofluorescence staining demonstrated that endogenous WWOX and SIMPLE co-localize to perinuclear compartments of MCF-7 human breast cancer cells. These studies demonstrate that WWOX contains a Group I WW domain that binds known cellular proteins containing the specific ligand PPXY. Identification and characterization of WWOX interacting proteins will lead to an understanding of the biological functions of WWOX in normal and tumor cells.

show abstract

“…Structure of the Tandem WW Domains of FBP21-Based on their ligand specificity, WW domains have been classified into four groups (45)(46)(47). Group I recognizes PPXY motifs, where X can be any residue; group II recognizes PPLP motifs; group III binds so-called PPR motifs, which represent stretches of prolines C-terminally flanked by an arginine; and group IV recognizes phospho-Ser or phospho-Thr followed by a proline.…”

Section: Discussionmentioning

confidence: 99%

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

Huang

Beullens

Zhang

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

Human FBP21 (formin-binding protein 21) contains a matrin-type zinc finger and two tandem WW domains. It is a component of the spliceosomes and interacts with several established splicing factors. Here we demonstrate for the first time that FBP21 is an activator of pre-mRNA splicing in vivo and that its splicing activation function and interaction with the splicing factor SIPP1 (splicing factor that interacts with PQBP1 and PP1) are both mediated by the two tandem WW domains of group III. We determined the solution structure of the tandem WW domains of FBP21 and found that the WW domains recognize peptide ligands containing either group II (PPLP) or group III (PPR) motifs. The binding interfaces involve both the XP and XP2 grooves of the two WW domains. Significantly, the tandem WW domains of FBP21 are connected by a highly flexible region, enabling their simultaneous interaction with two proline-rich motifs of SIPP1. The strong interaction between SIPP1 and FBP21 can be explained by the conjugation of two low affinity interactions with the tandem WW domains. Our study provides a structural basis for understanding the molecular mechanism underlying the functional implication of FBP21 and the biological specificity of tandem WW domains.Gene expression in eukaryotic cells involves several steps, including transcription, mRNA processing, and export. Pre-mRNA splicing takes place in the spliceosome, a highly dynamic ribonucleoprotein particle that consists of five small nuclear RNAs and at least 150 proteins. Small nuclear ribonucleoproteins (snRNPs) 3 and numerous protein factors are essential for the formation of the active spliceosome (1, 2). In budding yeast, the splicing factor Prp40 participates in crossintron bridging by interacting with the branch point-binding protein (BBP) and the U5 snRNP component Prp8. Prp40 contacts the 5Ј splice site and interacts with BBP, bringing the 5Ј splice site and the branch point in spatial proximity. These interactions are believed to be conserved in mammals (3-5). FBP21 (formin-binding protein 21), the mammalian Prp40-like protein, colocalizes with splicing factors in nuclear storage sites for pre-mRNA splicing factors. In addition, FBP21 is a component of the mammalian spliceosomal A/B complex and is associated with U2 snRNPs (6). FBP21 interacts directly with the splicing factors U1 snRNP protein U1C, the core snRNP proteins SmB and SmBЈ, and the branch point-binding protein SF1/mBBP, suggesting that it may also play a role in crossintron bridging of U1 and U2 snRNPs in the spliceosomes. FBP21 contains a matrin-type zinc finger and two group III WW domains ( Fig. 1) that are structurally related to those of the established splicing factors U1C and Prp40, respectively (6, 7). The binding of FBP21 to splicing factors is mediated by its tandem WW domains, which represent interaction modules for proline-rich ligands (4, 8, 9). Although the above data strongly suggest that FBP21 has a role in pre-mRNA splicing, there are no in vivo data to support this contention. The splicing...

show abstract

WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains

Cited by 123 publications

References 29 publications

Proline-rich Sequence Recognition

Proline-rich Sequence Recognition

WWOX binds the specific proline-rich ligand PPXY: identification of candidate interacting proteins

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

Contact Info

Product

Resources

About