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PDBsum entry 1zr7
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Signaling protein
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PDB id
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1zr7
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References listed in PDB file
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Key reference
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Title
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Solution structure and binding specificity of fbp11/hypa ww domain as group-Ii/III.
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Authors
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Y.Kato,
Y.Hino,
K.Nagata,
M.Tanokura.
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Ref.
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Proteins, 2006,
63,
227-234.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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).
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2006,
63,
227-234)
copyright 2006.
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