2B7E

First FF domain of Prp40 Yeast Protein

Summary for 2B7E

• Entry DOI: 10.2210/pdb2b7e/pdb
• NMR Information: BMRB: 6850
• Descriptor: Pre-mRNA processing protein PRP40 (1 entity in total)
• Functional Keywords: structural protein
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Nucleus: P33203
• Total number of polymer chains: 1
• Total formula weight: 7159.10

Authors

Gasch, A.,Wiesner, S.,Martin-Malpartida, P.,Ramirez-Espain, X.,Ruiz, L.,Macias, M.J. (deposition date: 2005-10-04, release date: 2005-11-01, Last modification date: 2024-05-22)

Primary citation

Gasch, A.,Wiesner, S.,Martin-Malpartida, P.,Ramirez-Espain, X.,Ruiz, L.,Macias, M.J.
The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
J.Biol.Chem., 281:356-364, 2006

PubMed Abstract: The yeast splicing factor Prp40 (pre-mRNA processing protein 40) consists of a pair of WW domains followed by several FF domains. The region comprising the FF domains has been shown to associate with the 5' end of U1 small nuclear RNA and to interact directly with two proteins, the Clf1 (Crooked neck-like factor 1) and the phosphorylated repeats of the C-terminal domain of RNA polymerase II (CTD-RNAPII). In this work we reported the solution structure of the first FF domain of Prp40 and the identification of a novel ligand-binding site in FF domains. By using chemical shift assays, we found a binding site for the N-terminal crooked neck tetratricopeptide repeat of Clf1 that is distinct and structurally separate from the previously identified CTD-RNAPII binding pocket of the FBP11 (formin-binding protein 11) FF1 domain. No interaction, however, was observed between the Prp40 FF1 domain and three different peptides derived from the CTD-RNAPII protein. Indeed, the equivalent CTD-RNAPII-binding site in the Prp40 FF1 domain is predominantly negatively charged and thus unfavorable for an interaction with phosphorylated peptide sequences. Sequence alignments and phylogenetic tree reconstructions using the FF domains of three functionally related proteins, Prp40, FBP11, and CA150, revealed that Prp40 and FBP11 are not orthologous proteins and supported the different ligand specificities shown by their respective FF1 domains. Our results also revealed that not all FF domains in Prp40 are functionally equivalent. We proposed that at least two different interaction surfaces exist in FF domains that have evolved to recognize distinct binding motifs.

PubMed: 16253993
DOI: 10.1074/jbc.M508047200

Experimental method

SOLUTION NMR