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PDBsum entry 1zr7

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protein links
Signaling protein PDB id
1zr7
Jmol
Contents
Protein chain
30 a.a. *
* Residue conservation analysis
PDB id:
1zr7
Name: Signaling protein
Title: Solution structure of the first ww domain of fbp11
Structure: Huntingtin-interacting protein hypa/fbp11. Chain: a. Fragment: residues in database 150-177. Synonym: formin binding protein 11 (fbp11)/huntingtin yeast partner a (hypa). Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: fbp11. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: Y.Kato,Y.Hino,M.Tanokura,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
Y.Kato et al. (2006). Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III. Proteins, 63, 227-234. PubMed id: 16463264 DOI: 10.1002/prot.20880
Date:
19-May-05     Release date:   30-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O75400  (PR40A_HUMAN) -  Pre-mRNA-processing factor 40 homolog A
Seq:
Struc:
 
Seq:
Struc:
957 a.a.
30 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1002/prot.20880 Proteins 63:227-234 (2006)
PubMed id: 16463264  
 
 
Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III.
Y.Kato, Y.Hino, K.Nagata, M.Tanokura.
 
  ABSTRACT  
 
The Group-II/III WW domains bind Pro-rich sequences, the most frequent protein motif found in eucaryotic genomes. We have proposed that the Group-II and -III WW domains be merged into a larger group because the members of each group have relatively wide specificity and bind to the common ligands [Kato et al., J Biol Chem 2004;279:31833-31841]. We have also proposed that Group-II/III has a common surface patch, the XP2 groove, to bind the ligands. The first WW domain of FBP11/HYPA is one of the Group-II/III WW domains. The solution structure of the 26 residue-long converged region exhibits an antiparallel triple stranded beta-sheet with a small hydrophobic core. The WW domain of FBP11/HYPA has both XP and XP2 grooves on its surface. Ligand titration by 1H-15N HSQC NMR spectra revealed that the WW domain of FBP11/HYPA binds all the peptides with the PL, PP, and PR motifs. The profile patterns of chemical shift perturbation were quite similar among the spectra titrated with all three ligands. In addition, the titration significantly shifts the signals of the residues that compose the XP2 groove. All these findings suggest the functional importance of the XP2 groove and group definition of Group-II/III of the WW domains.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Solution structure of FBP11 WW1. Superimposition of the best 20 structures out of 100 calculated structures of FBP11 WW1 from CYANA-2.0.
Figure 2.
Figure 2. Comparison of FBP11 WW1 to other Group-II/III WW domains. (A) Alignment of four WW domains that are similar to FBP11 WW1. The red characters show completely identical residues among these four proteins. We used residue numbering that we had defined previously to facilitate the comparison to other WW domains.[4] Based on this residue numbering system, we numbered the second Trp the 34th residue, which is the 168th in the entire FBP11/HYPA sequence. The arrows show the positions of the -strands that were predicted by CSI.[21] The intervals between strands were referred to as Loops I and II. (B) Superposition of backbones of the Group-II/III WW domains published so far, including the side chains of Trp12, Tyr24, and Pro37. The orange, pink, blue, and green bonds are the NMR mean structures of FBP11 WW1 by Pires and colleagues (PDB code: 1YWJ), FBP11 WW1 by the present authors (PDB code: 1ZR7), FBP28 WW2 (PDB code: 1E0L), and Prp40 WW1 (PDB code: 1O6W), respectively,[25][26] corresponding to the font colors in (A). The side chain of Pro18 of FBP11 WW1 was additionally depicted. The two sides of the WW domain sheet structure were defined, which are referred to as the binding side and backside. The drawing and fitting of the molecules were carried out with Swiss PDB viewer.[31] (C) Superposition of the backbones of the FBP11 WW1 structures by Pires and colleagues and the present authors from the different orientation from that in (B). The color code is the same as (B).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 227-234) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20208353 K.Nagata (2010).
Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.
  Biosci Biotechnol Biochem, 74, 462-470.  
19592703 X.Huang, M.Beullens, J.Zhang, Y.Zhou, E.Nicolaescu, B.Lesage, Q.Hu, J.Wu, M.Bollen, and Y.Shi (2009).
Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21).
  J Biol Chem, 284, 25375-25387.
PDB code: 2jxw
18074396 R.L.Rich, and D.G.Myszka (2007).
Survey of the year 2006 commercial optical biosensor literature.
  J Mol Recognit, 20, 300-366.  
17065151 Y.Kato, T.Miyakawa, J.Kurita, and M.Tanokura (2006).
Structure of FBP11 WW1-PL ligand complex reveals the mechanism of proline-rich ligand recognition by group II/III WW domains.
  J Biol Chem, 281, 40321-40329.
PDB code: 2dyf
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.