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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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Contents |
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* Residue conservation analysis
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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 of pafp-S: a new knottin-Type antifungal peptide from the seeds of phytolacca americana.
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Authors
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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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Ref.
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Biochemistry, 2001,
40,
10973-10978.
[DOI no: ]
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PubMed id
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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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