PDBsum entry 1ywi

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Structural protein PDB id
Protein chain
28 a.a. *
* Residue conservation analysis
PDB id:
Name: Structural protein
Title: Structure of the fbp11ww1 domain complexed to the peptide apptppplpp
Structure: Formin-binding protein 3. Chain: a. Fragment: ww1 domain. Synonym: formin binding protein 11. Engineered: yes. Formin. Chain: b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: automated solid phase synthesis on chlortrityl resin using fmoc strategy
NMR struc: 15 models
Authors: J.R.Pires,C.Parthier,R.Aido-Machado,U.Wiedemann,L.Otte, G.Boehm,R.Rudolph,H.Oschkinat
Key ref:
J.R.Pires et al. (2005). Structural basis for APPTPPPLPP peptide recognition by the FBP11WW1 domain. J Mol Biol, 348, 399-408. PubMed id: 15811376 DOI: 10.1016/j.jmb.2005.02.056
18-Feb-05     Release date:   12-Apr-05    
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Protein chain
Pfam   ArchSchema ?
O75400  (PR40A_HUMAN) -  Pre-mRNA-processing factor 40 homolog A
957 a.a.
28 a.a.
Key:    PfamA domain  Secondary structure


DOI no: 10.1016/j.jmb.2005.02.056 J Mol Biol 348:399-408 (2005)
PubMed id: 15811376  
Structural basis for APPTPPPLPP peptide recognition by the FBP11WW1 domain.
J.R.Pires, C.Parthier, R.Aido-Machado, U.Wiedemann, L.Otte, G.Böhm, R.Rudolph, H.Oschkinat.
WW domains are small protein-protein interaction modules that recognize proline-rich stretches in proteins. The class II tandem WW domains of the formin binding protein 11 (FBP11) recognize specifically proteins containing PPLPp motifs as present in the formins that are involved in limb and kidney development, and in the methyl-CpG-binding protein 2 (MeCP2), associated with the Rett syndrome. The interaction involves the specific recognition of a leucine side-chain. Here, we report on the novel structure of the complex formed by the FPB11WW1 domain and the formin fragment APPTPPPLPP revealing the specificity determinants of class II WW domains.
  Selected figure(s)  
Figure 1.
Figure 1. The WW domain sequences and classes. Amino acid sequence of selected WW domains grouped in classes according to ligand specificity.4 Classes/ligand motifs: class II PPLPp (magenta), class III (p/ )P(p/g)PPpR or (p/ )PPRgpPp (orange), class IV (poS/poT)P (green) and class I PPxY (blue). Conserved amino acid residues are in bold; amino acid residues on the b-strand face where binding occurs are grey-shaded; amino acid residues responsible for class specificity are colored. The asterisk (*) indicates sequences assumed to be FBP11 orthologs.
Figure 4.
Figure 4. Comparison of WW and SH3 domain complexes. (a) Schematic representation of a WW domain showing important regions for ligand recognition. Residues conserved for all WW domains are displayed in blue. Positions changing between the WW domain specificity classes are shown in green, next to which the amino acid types and their corresponding WW domain classes are indicated in parentheses. Superposition of FBP11WW1 (grey ribbon, blue side-chains, class II) complexed to APPTPPPLPP (cyan) with: (b) dystrophinWW domain (red, class I) in complex with SPPPY (yellow); (c) Pin1WW domain (red, class IV): in complex with (poS)PT(poS)PS (yellow); and (d) the C-CRK N-terminal SH3 domain (red) in complex with PPPALPPK (yellow). (e) PRP40WW1 (red, class II) and (f) PRP40WW2 (red, class II)
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 399-408) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
18820302 J.Singh, A.Saxena, J.Christodoulou, and D.Ravine (2008).
MECP2 genomic structure and function: insights from ENCODE.
  Nucleic Acids Res, 36, 6035-6047.  
17437719 B.Morales, X.Ramirez-Espain, A.Z.Shaw, P.Martin-Malpartida, F.Yraola, E.Sánchez-Tilló, C.Farrera, A.Celada, M.Royo, and M.J.Macias (2007).
NMR structural studies of the ItchWW3 domain reveal that phosphorylation at T30 inhibits the interaction with PPxY-containing ligands.
  Structure, 15, 473-483.
PDB codes: 2jo9 2joc
17355961 M.Brucet, J.Querol-Audí, M.Serra, X.Ramirez-Espain, K.Bertlik, L.Ruiz, J.Lloberas, M.J.Macias, I.Fita, and A.Celada (2007).
Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains.
  J Biol Chem, 282, 14547-14557.
PDB codes: 2o4g 2o4i
17686488 M.Meiyappan, G.Birrane, and J.A.Ladias (2007).
Structural basis for polyproline recognition by the FE65 WW domain.
  J Mol Biol, 372, 970-980.
PDB codes: 2ho2 2idh 2oei
16807295 M.Jäger, Y.Zhang, J.Bieschke, H.Nguyen, M.Dendle, M.E.Bowman, J.P.Noel, M.Gruebele, and J.W.Kelly (2006).
Structure-function-folding relationship in a WW domain.
  Proc Natl Acad Sci U S A, 103, 10648-10653.
PDB codes: 1zcn 2f21
16827924 M.K.Kalita, G.Ramasamy, S.Duraisamy, V.S.Chauhan, and D.Gupta (2006).
ProtRepeatsDB: a database of amino acid repeats in genomes.
  BMC Bioinformatics, 7, 336.  
16531238 V.Kanelis, M.C.Bruce, N.R.Skrynnikov, D.Rotin, and J.D.Forman-Kay (2006).
Structural determinants for high-affinity binding in a Nedd4 WW3* domain-Comm PY motif complex.
  Structure, 14, 543-553.
PDB code: 2ez5
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
16463264 Y.Kato, Y.Hino, K.Nagata, and M.Tanokura (2006).
Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III.
  Proteins, 63, 227-234.
PDB code: 1zr7
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.