PDBsum entry 2juc

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protein links
Unknown function PDB id
Protein chain
55 a.a. *
* Residue conservation analysis
PDB id:
Name: Unknown function
Title: Urn1 ff domain yeast
Structure: Pre-mRNA-splicing factor urn1. Chain: a. Fragment: ff domain (residues 212-266). Synonym: u2-u5-u6 snrnp, res complex and ntc-interacting pre-mRNA-splicing factor 1. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Gene: urn1. Expressed in: escherichia coli.
NMR struc: 15 models
Authors: R.Bonet,X.Ramirez-Espain,M.J.Macias
Key ref:
R.Bonet et al. (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. PubMed id: 18536009 DOI: 10.1002/prot.22127
21-Aug-07     Release date:   17-Jun-08    
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Protein chain
Pfam   ArchSchema ?
Q06525  (URN1_YEAST) -  Pre-mRNA-splicing factor URN1
465 a.a.
55 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1002/prot.22127 Proteins 73:1001-1009 (2008)
PubMed id: 18536009  
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.
R.Bonet, X.Ramirez-Espain, M.J.Macias.
FF domains are present in three protein families: the splicing factors formin binding protein 11 (FBP11), Prp40, and URN1, the transcription factor CA150, and the p190RhoGTPase-related proteins. This simplicity in distribution, however, is contrasted by the difficulty in defining their biological role. At best, the group of ligand FF domains can bind to form a motley crew with binding reports pointing also to negative/aromatic sequences, the tetratricopeptide repeat, the transcription factor TFII-I and even to RNA. To expand our knowledge on the FF domain, we selected the FF domain present in the URN1 yeast splicing factor as the subject for structural studies. The URN1 protein is one of the two known proteins containing only one FF domain, making it the most simplified representative of FF domain-containing splicing factors. The solution structure reveals that the domain adopts the classical FF fold, with a distinctive negatively charged patch on its surface. All available FF structures have a well-conserved fold but variable electrostatic patches on their surfaces. These patches are unconserved, even for domains with similar pK(a)s. To investigate potential binding sites in FF domains, we performed structural comparisons to other proteins with similar folds. In addition to the structures detected by SCOP, we included SURP domains, which also adopt the alpha1-alpha2-3(10)-alpha3 architecture. We observed that the main difference between all these structures resides in the orientation of the second helix. Remarkably, in DEK, SURP, and Prp40FF1 structures (the exception is the FBP11FF1 domain), the second helix participates in ligand recognition. Furthermore, SURP and Prp40FF1 binding sites also include the 3(10) helix, which forms a partially exposed hydrophobic cavity. This cavity is also present in at least CA150FF1 and FF2 structures. Thus, as with WW domains, the FF fold seems to have developed binding-site variations to accommodate an abundant and variable set of ligands. Proteins 2008. (c) 2008 Wiley-Liss, Inc.
  Selected figure(s)  
Figure 1.
Figure 1. URN1FF structure determined by NMR. (A) Stereo view of the overlay of the backbone atoms of URN1FF 15 lowest energy structures after water refinement. (B) Ribbon representation of the lowest-energy structure showing the side chains for the hydrophobic residues that form the domain's core. The two conserved Phe that give name to the domain are depicted in green. (C) URN1FF domain (in green) superimposed to the lowest energy structure of the different FF domains for which the structure is deposited in the PDB. Color codes for the remaining FF domains are as follows: scPrp40FF1, red; hFBP11FF1, violet; hFBP11FF5, pale green; hCA150FF1, light blue; hCA150FF3, pink; hCA150FF4, orange. The corresponding PDB codes are scPrp40FF1-2B7E, hFBP11FF1-1UZC, hFBP11FF5-2CQN, hCA150FF1-2DOD, hCA150FF3-2DOE, and hCA150FF4-2DOF. (D) RMSD of the different FF domains with respect to the URN1FF. Fittings were generated taking either the secondary structure elements ( 1- 2- 3 helices) or the whole molecules (Global).
Figure 3.
Figure 3. Structural comparison between the URN1FF domain and other related structures. (A) Structure-based alignment of FF and SURP aligned profiles. Conserved residues between the two profiles are indicated with red gradient (FFs) and blue gradient (SURPs) backgrounds according to the degree of conservation (dark is the most conserved). For instance, in the FF family the Phe in the first helix (the one corresponding to the first Phe in the name FF) is conserved in all sequences, while the SURP family contains an Ala at this equivalent position. Both families have a pair of hydrophobic semiconserved residues in position +3 with respect to this Phe/Ala highly conserved residue. Similarly, in the last helix there are four positions conserved in each family, but not between the families. Secondary structure elements for each profile and residue numbers of the distinct domains are indicated. (B) Left and right: URN1FF domain (in orange) superimposed to either DEK C-term structure (in green, PDB code 1Q1V) or the SF3a120SURP1 structure (in blue, PDB code 2DT6). Representations show the superimpositions according to the 1- 3 fittings using the optAlign alignment script. Secondary structure elements are indicated. (C) RMSD of the family representatives for another 3-helical bundle fold, as well as for the SF3a120SURP1 domain (in bold) with respect to the URN1FF. Fittings were generated taking either the secondary structure elements 1- 3 helices or the whole molecules (Global). PDB codes: C-term S/T phosphatase 2C-1A6Q, B-form DNA-mimic Ocr-1S7Z, DEK-C-term-1Q1V, IscX protein-1UJ8, SF3a120SURP1-2DT6.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 73, 1001-1009) copyright 2008.  
  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.  
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