 |
PDBsum entry 1k9q
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Structural protein
|
PDB id
|
|
|
|
1k9q
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Solution structures of the yap65 ww domain and the variant l30 k in complex with the peptides gtppppytvg, N-(N-Octyl)-Gpppy and plppy and the application of peptide libraries reveal a minimal binding epitope.
|
|
|
Authors
|
|
J.R.Pires,
F.Taha-Nejad,
F.Toepert,
T.Ast,
U.Hoffmüller,
J.Schneider-Mergener,
R.Kühne,
M.J.Macias,
H.Oschkinat.
|
|
|
Ref.
|
|
J Mol Biol, 2001,
314,
1147-1156.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The single mutation L30 K in the Hu-Yap65 WW domain increased the stability of
the complex with the peptide GTPPPPYTVG (K(d)=40(+/-5) microM). Here we report
the refined solution structure of this complex by NMR spectroscopy and further
derived structure-activity relationships by using ligand peptide libraries with
truncated sequences and a substitution analysis that yielded acetyl-PPPPY as the
smallest high-affinity binding peptide (K(d)=60 microM). The structures of two
new complexes with weaker binding ligands chosen based on these results
(N-(n-octyl)-GPPPYNH(2) and Ac-PLPPY) comprising the wild-type WW domain of
Hu-Yap65 were determined. Comparison of the structures of the three complexes
were useful for identifying the molecular basis of high-affinity: hydrophobic
and specific interactions between the side-chains of Y28 and W39 and P5' and
P4', respectively, and hydrogen bonds between T37 (donnor) and P5' (acceptor)
and between W39 (donnor) and T2' (acceptor) stabilize the complex.The structure
of the complex L30 K Hu-Yap65 WW domain/GTPPPPYTVG is compared to the published
crystal structure of the dystrophin WW domain bound to a segment of the
beta-dystroglycan protein and to the solution structure of the first Nedd4 WW
domain and its prolin-rich ligand, suggesting that WW sequences bind
proline-rich peptides in an evolutionary conserved fashion. The position
equivalent to T22 in the Hu-Yap65 WW domain sequence is seen as responsible for
differentiation in the binding mode among the WW domains of group I.
|
|
|
|
|
|
|
|
Figure 4.
Figure 4. (a) Cartoon representation of the structure of
the the complex L30K Hu-Yap WW domain/GTPPPPYTVG. (b)
Poly-proline peptide bound to the surface of the L30K Hu-Yap65
WW domain; the surface is coloured by lipophilicity, in brown
the more lipophilic regions and in green more hydrophilic.
Hydrogen bond donnors are coloured red.
|
|
Figure 5.
Figure 5. Comparison of the structures. (a) Superposition
of the structures of the complexes of the Hu-Yap65 WW domain:
L30 K WW domain and the peptide GTPPPPYTVG (black), wild-type WW
domain and the petide N-(n-octyl)-GPPPY-NH[2] (green) and
wild-type WW domain and the peptide acetyl-PLPPY (magenta). (b)
L30K WW domain of the Hu-Yap65 and the peptide GTPPPPYTVG
(complex 1, black) superimposed to the complex formed by the WW
domain of dystrophin and a poly-proline containing fragment of
dystroglican (blue). (c) L30K WW domain of the Hu-Yap65 and the
peptide GTPPPPYTVG (complex 1, black) superimposed to the
complex formed by the WW domain of Nedd4 and its proline-rich
ligand (red). The structures were superimposed by the a-carbon
atoms of the residues that compose the binding pocket (T22, Y28,
L30 or K30, H32, Q35, T37 and W39) and are the only residues
displayed together with the ligands.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
314,
1147-1156)
copyright 2001.
|
|
|
|
|
|
|
