PDBsum entry 2b7e

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protein links
Structural protein PDB id
Protein chain
59 a.a. *
* Residue conservation analysis
PDB id:
Name: Structural protein
Title: First ff domain of prp40 yeast protein
Structure: Pre-mRNA processing protein prp40. Chain: a. Fragment: ff1 domain (residues 134-189). Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: prp40. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 12 models
Authors: A.Gasch,S.Wiesner,P.Martin-Malpartida,X.Ramirez-Espain, L.Ruiz,M.J.Macias
Key ref:
A.Gasch et al. (2006). 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. PubMed id: 16253993 DOI: 10.1074/jbc.M508047200
04-Oct-05     Release date:   01-Nov-05    
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Protein chain
Pfam   ArchSchema ?
P33203  (PRP40_YEAST) -  Pre-mRNA-processing protein PRP40
583 a.a.
59 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)


DOI no: 10.1074/jbc.M508047200 J Biol Chem 281:356-364 (2006)
PubMed id: 16253993  
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.
A.Gasch, S.Wiesner, P.Martin-Malpartida, X.Ramirez-Espain, L.Ruiz, M.J.Macias.
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.
  Selected figure(s)  
Figure 1.
FIGURE 1. Solution structure of the Prp40 FF1 domain. A, stereoview of the best fit backbone (N, C^ ,C') superposition of the 15 lowest energy structures after water refinement. B, ribbon representation of the lowest energy structure with secondary structure elements. Conserved aromatic residues in the core of the domain are depicted. Residue numbers of labeled side chains correspond to their position in the full-length Prp40 protein. C, ribbon representation of the superimposed structures of the Prp40 FF1 domain (dark gray) and the HYPA/FBP11 FF1 domain (light gray) (Protein Data Bank entry 1uzc).
Figure 4.
FIGURE 4. Comparison of the Prp40 FF1 and FF2 and the HYPA/FBP11 FF1 electrostatic surface potential. All surface representations on the left side are shown in an orientation identical to that in Fig. 2B; the right side representations are rotated 90°. A, electrostatic surface potential of the Prp40 FF1 domain. B, electrostatic surface potential of the HYPA/FBP11 FF1 domain. The RNAPII CTD-binding site is indicated by a black line in the panel on the right side. C, electrostatic surface potential of the Prp40 FF2 domain model. The S240F suppressor mutation is highlighted in green.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 356-364) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19722265 R.Bonet, L.Ruiz, B.Morales, and M.J.Macias (2009).
Solution structure of the fourth FF domain of yeast Prp40 splicing factor.
  Proteins, 77, 1000-1003.
PDB code: 2kfd
19014439 C.Ester, and P.Uetz (2008).
The FF domains of yeast U1 snRNP protein Prp40 mediate interactions with Luc7 and Snu71.
  BMC Biochem, 9, 29.  
18375978 Q.Wang, L.Zhang, B.Lynn, and B.C.Rymond (2008).
A BBP-Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast.
  Nucleic Acids Res, 36, 2787-2798.  
18536009 R.Bonet, X.Ramirez-Espain, and M.J.Macias (2008).
Solution structure of the yeast URN1 splicing factor FF domain: comparative analysis of charge distributions in FF domain structures-FFs and SURPs, two domains with a similar fold.
  Proteins, 73, 1001-1009.
PDB code: 2juc
17178401 G.Edenfeld, G.Volohonsky, K.Krukkert, E.Naffin, U.Lammel, A.Grimm, D.Engelen, A.Reuveny, T.Volk, and C.Klämbt (2006).
The splicing factor crooked neck associates with the RNA-binding protein HOW to control glial cell maturation in Drosophila.
  Neuron, 52, 969-980.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.