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PDBsum entry 1dkc
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Antifungal protein
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PDB id
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1dkc
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DOI no:
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Biochemistry
40:10973-10978
(2001)
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PubMed id:
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Solution structure of PAFP-S: a new knottin-type antifungal peptide from the seeds of Phytolacca americana.
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G.H.Gao,
W.Liu,
J.X.Dai,
J.F.Wang,
Z.Hu,
Y.Zhang,
D.C.Wang.
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ABSTRACT
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The three-dimensional solution structure of PAFP-S, an antifungal peptide
extracted from the seeds of Phytolacca americana, was determined using 1H NMR
spectroscopy. This cationic peptide contains 38 amino acid residues. Its
structure was determined from 302 distance restraints and 36 dihedral restraints
derived from NOEs and coupling constants. The peptide has six cysteines involved
in three disulfide bonds. The previously unassigned parings have now been
determined from NMR data. The solution structure of PAFP-S is presented as a set
of 20 structures using ab initio dynamic simulated annealing, with an average
RMS deviation of 1.68 A for the backbone heavy atoms and 2.19 A for all heavy
atoms, respectively. For the well-defined triple-stranded beta-sheet involving
residues 8-10, 23-27, and 32-36, the corresponding values were 0.39 and 1.25 A.
The global fold involves a cystine-knotted three-stranded antiparallel
beta-sheet (residues 8-10, 23-27, 32-36), a flexible loop (residues 14-19), and
four beta-reverse turns (residues 4-8, 11-14, 19-22, 28-32). This structure
features all the characteristics of the knottin fold. It is the first structural
model of an antifungal peptide that adopts a knottin-type structure. PAFP-S has
an extended hydrophobic surface comprised of residues Tyr23, Phe25, Ile27,
Tyr32, and Val34. The side chains of these residues are well-defined in the NMR
structure. Several hydrophilic and positively charged residues (Arg9, Arg38, and
Lys36) surround the hydrophobic surface, giving PAFP-S an amphiphilic character
which would be the main structural basis of its biological function.
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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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A.J.De Lucca,
T.E.Cleveland,
and
D.E.Wedge
(2005).
Plant-derived antifungal proteins and peptides.
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Can J Microbiol,
51,
1001-1014.
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M.Shmulevitz,
R.F.Epand,
R.M.Epand,
and
R.Duncan
(2004).
Structural and functional properties of an unusual internal fusion peptide in a nonenveloped virus membrane fusion protein.
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J Virol,
78,
2808-2818.
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F.Barbault,
C.Landon,
M.Guenneugues,
J.P.Meyer,
V.Schott,
J.L.Dimarcq,
and
F.Vovelle
(2003).
Solution structure of Alo-3: a new knottin-type antifungal peptide from the insect Acrocinus longimanus.
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Biochemistry,
42,
14434-14442.
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PDB code:
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Y.Xiang,
R.H.Huang,
W.Liu,
G.P.Li,
X.Z.Liu,
and
D.C.Wang
(2002).
Crystallization and preliminary crystallographic studies of a novel antifungal protein with five disulfide bridges from Eucommia ulmoides Oliver.
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Acta Crystallogr D Biol Crystallogr,
58,
1838-1840.
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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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