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PDBsum entry 2idh

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protein ligands Protein-protein interface(s) links
Protein binding PDB id
2idh
Jmol
Contents
Protein chains
30 a.a. *
31 a.a. *
34 a.a. *
33 a.a. *
Ligands
SO4 ×2
PG4 ×7
Waters ×119
* Residue conservation analysis
PDB id:
2idh
Name: Protein binding
Title: Crystal structure of human fe65 ww domain
Structure: Amyloid beta a4 protein-binding family b member 1. Chain: a, b, c, d, e, f, g, h. Fragment: ww domain. Synonym: fe65 protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: apbb1, fe65. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.28Å     R-factor:   0.220     R-free:   0.282
Authors: M.Meiyappan,G.Birrane,J.A.A.Ladias
Key ref:
M.Meiyappan et al. (2007). Structural Basis for Polyproline Recognition by the FE65 WW Domain. J Mol Biol, 372, 970-980. PubMed id: 17686488 DOI: 10.1016/j.jmb.2007.06.064
Date:
15-Sep-06     Release date:   10-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O00213  (APBB1_HUMAN) -  Amyloid beta A4 precursor protein-binding family B member 1
Seq:
Struc:
 
Seq:
Struc:
710 a.a.
30 a.a.
Protein chains
Pfam   ArchSchema ?
O00213  (APBB1_HUMAN) -  Amyloid beta A4 precursor protein-binding family B member 1
Seq:
Struc:
 
Seq:
Struc:
710 a.a.
31 a.a.
Protein chain
Pfam   ArchSchema ?
O00213  (APBB1_HUMAN) -  Amyloid beta A4 precursor protein-binding family B member 1
Seq:
Struc:
 
Seq:
Struc:
710 a.a.
34 a.a.*
Protein chain
Pfam   ArchSchema ?
O00213  (APBB1_HUMAN) -  Amyloid beta A4 precursor protein-binding family B member 1
Seq:
Struc:
 
Seq:
Struc:
710 a.a.
33 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1016/j.jmb.2007.06.064 J Mol Biol 372:970-980 (2007)
PubMed id: 17686488  
 
 
Structural Basis for Polyproline Recognition by the FE65 WW Domain.
M.Meiyappan, G.Birrane, J.A.Ladias.
 
  ABSTRACT  
 
The neuronal protein FE65 functions in brain development and amyloid precursor protein (APP) signaling through its interaction with the mammalian enabled (Mena) protein and APP, respectively. The recognition of short polyproline sequences in Mena by the FE65 WW domain has a central role in axon guidance and neuronal positioning in the developing brain. We have determined the crystal structures of the human FE65 WW domain (residues 253-289) in the apo form and bound to the peptides PPPPPPLPP and PPPPPPPPPL, which correspond to human Mena residues 313-321 and 347-356, respectively. The FE65 WW domain contains two parallel ligand-binding grooves, XP (formed by residues Y269 and W280) and XP2 (formed by Y269 and W271). Both Mena peptides adopt a polyproline helical II conformation and bind to the WW domain in a forward (N-C) orientation through selection of the PPPPP motif by the XP and XP2 grooves. This mode of ligand recognition is strikingly similar to polyproline interaction with SH3 domains. Importantly, comparison of the FE65 WW structures in the apo and liganded forms shows that the XP2 groove is formed by an induced-fit mechanism that involves movements of the W271 and Y269 side-chains upon ligand binding. These structures elucidate the molecular determinants underlying polyproline ligand selection by the FE65 WW domain and provide a framework for the design of small molecules that would interfere with FE65 WW-ligand interaction and modulate neuronal development and APP signaling.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Sequence comparison of representative WW domains. The sequences of the single WW of FE65, dystrophin, and Pin1, the first WW of FBP11, PRP40, YAP65, and Nedd4, and the second WW of FBP28, were aligned using the program CLUSTAL W.^56 Hyphens represent gaps inserted for optimum alignment. The secondary structure elements of FE65 WW are indicated at the top. Residues of human FE65 are numbered. Two conserved tryptophan residues (after which the domain is named) are shown in white on a blue background. Invariant tyrosine residues (shown in white on a red background) and bulky hydrophobic residues (highlighted in yellow) form the XP2 groove in group II/III domains. Conserved threonine/serine residues that hydrogen bond with the ligand are highlighted in green. (b) Ribbon diagram of the FE65 WW domain. Residues that form the XP and XP2 groves are shown as yellow stick models. The side-chains of residues forming a hydrophobic core that stabilizes the fold are shown in pink. (c) A stereo view of eight FE65 WW molecules present in the asymmetric unit. Superposition of these independent structures shows that they fall into two distinct conformations highlighted in shades of green (apo form) and pink (bound to a PEG400 molecule). Note the conformational changes of the W271 and Y269 side-chains in the bound form. (d) In the apo form, the XP2 groove is shallow. (e) Binding of a PEG400 molecule induces the formation of a deep XP2 groove, primarily through conformational changes of the indole side-chain of W271 and, to a lesser degree, of the phenyl ring of Y269. The Figure was made using PyMol [www.pymol.org].
Figure 4.
Figure 4. (a) Surface representation of the FE65 WW bound to the Mn10 peptide (shown as a stick model). Semitransparent rectangles denote the parallel orientation of the XP and XP2 grooves. (b) A diagram of the FE65 WW bound to Mn10 PPII helix (shown as a triangular prism), illustrating the parallel arrangement of the XP and XP2 grooves, the three aromatic residues that form them, and the proline residues of the ligand that occupy them (orange spheres). Unbound proline and leucine residues are shown as gray and cyan spheres, respectively. (c) Surface representation of the FBP11 WW1 bound to PPLP sequence (PDB code 2DYF), showing the non-parallel arrangement of the XP and XP2 grooves (rectangles). (d) Surface representation of the Abl tyrosine kinase SH3 domain bound to the peptide 3BP1 containing the sequence PPLPP (PDB code 1ABO), showing the parallel XP and XP2 grooves (rectangles). (e) A stereo view of the FE65 WW–Mn10 structure superimposed on the Abl SH3–3BP1 complex, showing the similar mode of PPII recognition by the aromatic triad of WW (yellow) and SH3 (light green) domains. The Mn10 and 3BP1 peptides are shown in cyan and pink, respectively.
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 372, 970-980) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19860855 B.H.Cool, G.Zitnik, G.M.Martin, and Q.Hu (2010).
Structural and functional characterization of a novel FE65 protein product up-regulated in cognitively impaired FE65 knockout mice.
  J Neurochem, 112, 410-419.  
  20944208 D.Das, N.V.Grishin, A.Kumar, D.Carlton, C.Bakolitsa, M.D.Miller, P.Abdubek, T.Astakhova, H.L.Axelrod, P.Burra, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, D.Ernst, C.L.Farr, J.Feuerhelm, A.Grzechnik, S.K.Grzechnik, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1174-1181.
PDB code: 3dee
20841568 J.Colicelli (2010).
ABL tyrosine kinases: evolution of function, regulation, and specificity.
  Sci Signal, 3, re6.  
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.  
20095050 S.D.Köhler, A.Weber, S.P.Howard, W.Welte, and M.Drescher (2010).
The proline-rich domain of TonB possesses an extended polyproline II-like conformation of sufficient length to span the periplasm of Gram-negative bacteria.
  Protein Sci, 19, 625-630.  
20806220 T.A.Jowitt, A.D.Murdoch, C.Baldock, R.Berry, J.M.Day, and T.E.Hardingham (2010).
Order within disorder: aggrecan chondroitin sulphate-attachment region provides new structural insights into protein sequences classified as disordered.
  Proteins, 78, 3317-3327.  
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
18833287 J.Radzimanowski, B.Simon, M.Sattler, K.Beyreuther, I.Sinning, and K.Wild (2008).
Structure of the intracellular domain of the amyloid precursor protein in complex with Fe65-PTB2.
  EMBO Rep, 9, 1134-1140.
PDB codes: 3dxc 3dxd 3dxe
  18453713 J.Radzimanowski, K.Beyreuther, I.Sinning, and K.Wild (2008).
Overproduction, purification, crystallization and preliminary X-ray analysis of human Fe65-PTB2 in complex with the amyloid precursor protein intracellular domain.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 409-412.  
18972023 L.Biedermannova, K.E Riley, K.Berka, P.Hobza, and J.Vondrasek (2008).
Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane.
  Phys Chem Chem Phys, 10, 6350-6359.  
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.