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PDBsum entry 1vj6
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Hydrolase/signaling protein
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PDB id
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1vj6
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References listed in PDB file
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Key reference
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Title
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Demonstration of long-Range interactions in a pdz domain by nmr, Kinetics, And protein engineering.
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Authors
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S.Gianni,
T.Walma,
A.Arcovito,
N.Calosci,
A.Bellelli,
A.Engström,
C.Travaglini-Allocatelli,
M.Brunori,
P.Jemth,
G.W.Vuister.
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Ref.
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Structure, 2006,
14,
1801-1809.
[DOI no: ]
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PubMed id
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Abstract
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Understanding the basis of communication within protein domains is a major
challenge in structural biology. We present structural and dynamical evidence
for allosteric effects in a PDZ domain, PDZ2 from the tyrosine phosphatase
PTP-BL, upon binding to a target peptide. The NMR structures of its free and
peptide-bound states differ in the orientation of helix alpha2 with respect to
the remainder of the molecule, concomitant with a readjustment of the
hydrophobic core. Using an ultrafast mixing instrument, we detected a deviation
from simple bimolecular kinetics for the association with peptide that is
consistent with a rate-limiting conformational change in the protein (k(obs)
approximately 7 x 10(3) s(-1)) and an induced-fit model. Furthermore, the
binding kinetics of 15 mutants revealed that binding is regulated by long-range
interactions, which can be correlated with the structural rearrangements
resulting from peptide binding. The homologous protein PSD-95 PDZ3 did not
display a similar ligand-induced conformational change.
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Figure 1.
Figure 1. Structures of PDZ Domains
(A) Overlay of the
ensemble of 35 NMR-derived structures of the PDZ2-peptide
complex colored as a rainbow ramp ranging from blue (N terminus)
to red (C terminus). The peptide is shown in stick
representation. For clarity, only the last five C-terminal
residues of the peptide are displayed.
(B) Superposition of
the structures of PDZ2 in the free (green, helix α2 in pink,
PDB code 1GM1) and complexed (blue, helix α2 in cyan, peptide
in red) states.
(C) Superposition between the structures of
PDZ3 in the free and complexed states (PDB codes 1BFE and 1BE9,
respectively). Color coding as in (B).
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Figure 4.
Figure 4. Peptide Binding to Mutant PDZ Domains
Stopped-flow data on representative mutants of PDZ domains.
Mutants were classified into three categories: those primarily
altering the association rate constant (A), the dissociation
rate constant (B), or both (C). See Table 2 for rate constants.
(D) Effect of mutagenesis on binding. PDZ2 is shown in ribbon
representation (gray); residues affected by mutagenesis in
space-filling representation. Blue-colored residues primarily
alter the association rate constant, salmon-colored residues
affect the dissociation rate constant, whereas magenta-colored
residues affect both rate constants. The P[−3]-P[0] residues
of the APC-peptide are also shown in red by using stick
representation.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
1801-1809)
copyright 2006.
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