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PDBsum entry 2kcf
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* Residue conservation analysis
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Enzyme class:
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E.C.5.2.1.8
- peptidylprolyl isomerase.
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Reaction:
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[protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)
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Peptidylproline (omega=180)
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=
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peptidylproline (omega=0)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Biopolymers
63:111-121
(2002)
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PubMed id:
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NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1.
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J.A.Kowalski,
K.Liu,
J.W.Kelly.
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ABSTRACT
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The NMR solution structure of the isolated Apo Pin1 WW domain (6-39) reveals
that it adopts a twisted three-stranded antiparallel beta-sheet conformation,
very similar to the structure exhibited by the crystal of this domain in the
context of the two domain Pin1 protein. While the B factors in the apo x-ray
crystal structure indicate that loop 1 and loop 2 are conformationally well
defined, the solution NMR data suggest that loop 1 is quite flexible, at least
in the absence of the ligand. The NMR chemical shift and nuclear Overhauser
effect pattern exhibited by the 6-39 Pin1 WW domain has proven to be diagnostic
for demonstrating that single site variants of this domain adopt a normally
folded structure. Knowledge of this type is critical before embarking on
time-consuming kinetic and thermodynamic studies required for a detailed
understanding of beta-sheet folding.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.M.Rogers,
L.G.Lippert,
and
F.Gai
(2010).
Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications.
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Anal Biochem,
399,
182-189.
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A.A.Fuller,
D.Du,
F.Liu,
J.E.Davoren,
G.Bhabha,
G.Kroon,
D.A.Case,
H.J.Dyson,
E.T.Powers,
P.Wipf,
M.Gruebele,
and
J.W.Kelly
(2009).
Evaluating beta-turn mimics as beta-sheet folding nucleators.
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Proc Natl Acad Sci U S A,
106,
11067-11072.
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PDB code:
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M.Jäger,
M.Dendle,
and
J.W.Kelly
(2009).
Sequence determinants of thermodynamic stability in a WW domain--an all-beta-sheet protein.
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Protein Sci,
18,
1806-1813.
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M.Jager,
S.Deechongkit,
E.K.Koepf,
H.Nguyen,
J.Gao,
E.T.Powers,
M.Gruebele,
and
J.W.Kelly
(2008).
Understanding the mechanism of beta-sheet folding from a chemical and biological perspective.
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Biopolymers,
90,
751-758.
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Z.Luo,
J.Ding,
and
Y.Zhou
(2008).
Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations.
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J Chem Phys,
128,
225103.
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C.S.Rapp,
T.Strauss,
A.Nederveen,
and
G.Fuentes
(2007).
Prediction of protein loop geometries in solution.
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Proteins,
69,
69-74.
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M.Jäger,
H.Nguyen,
M.Dendle,
M.Gruebele,
and
J.W.Kelly
(2007).
Influence of hPin1 WW N-terminal domain boundaries on function, protein stability, and folding.
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Protein Sci,
16,
1495-1501.
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M.Jäger,
M.Dendle,
A.A.Fuller,
and
J.W.Kelly
(2007).
A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function.
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Protein Sci,
16,
2306-2313.
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T.Peng,
J.S.Zintsmaster,
A.T.Namanja,
and
J.W.Peng
(2007).
Sequence-specific dynamics modulate recognition specificity in WW domains.
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Nat Struct Mol Biol,
14,
325-331.
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T.Sharpe,
A.L.Jonsson,
T.J.Rutherford,
V.Daggett,
and
A.R.Fersht
(2007).
The role of the turn in beta-hairpin formation during WW domain folding.
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Protein Sci,
16,
2233-2239.
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Z.Luo,
J.Ding,
and
Y.Zhou
(2007).
Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model.
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Biophys J,
93,
2152-2161.
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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.
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Proc Natl Acad Sci U S A,
103,
10648-10653.
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PDB codes:
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Y.Fu,
J.Gao,
J.Bieschke,
M.A.Dendle,
and
J.W.Kelly
(2006).
Amide-to-E-olefin versus amide-to-ester backbone H-bond perturbations: Evaluating the O-O repulsion for extracting H-bond energies.
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J Am Chem Soc,
128,
15948-15949.
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C.S.Rapp,
and
R.M.Pollack
(2005).
Crystal packing effects on protein loops.
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Proteins,
60,
103-109.
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S.Deechongkit,
H.Nguyen,
E.T.Powers,
P.E.Dawson,
M.Gruebele,
and
J.W.Kelly
(2004).
Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics.
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Nature,
430,
101-105.
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C.M.Kraemer-Pecore,
J.T.Lecomte,
and
J.R.Desjarlais
(2003).
A de novo redesign of the WW domain.
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Protein Sci,
12,
2194-2205.
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D.M.Jacobs,
K.Saxena,
M.Vogtherr,
P.Bernado,
M.Pons,
and
K.M.Fiebig
(2003).
Peptide binding induces large scale changes in inter-domain mobility in human Pin1.
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J Biol Chem,
278,
26174-26182.
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H.Nguyen,
M.Jager,
A.Moretto,
M.Gruebele,
and
J.W.Kelly
(2003).
Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation.
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Proc Natl Acad Sci U S A,
100,
3948-3953.
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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.
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Links
