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PDBsum entry 1iyc
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Antifungal protein
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PDB id
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1iyc
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References listed in PDB file
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Key reference
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Title
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Structural basis for new pattern of conserved amino acid residues related to chitin-Binding in the antifungal peptide from the coconut rhinoceros beetle oryctes rhinoceros.
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Authors
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H.Hemmi,
J.Ishibashi,
T.Tomie,
M.Yamakawa.
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Ref.
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J Biol Chem, 2003,
278,
22820-22827.
[DOI no: ]
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PubMed id
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Abstract
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Scarabaecin isolated from hemolymph of the coconut rhinoceros beetle Oryctes
rhinoceros is a 36-residue polypeptide that has antifungal activity. The
solution structure of scarabaecin has been determined from twodimensional 1H NMR
spectroscopic data and hybrid distance geometry-simulated annealing protocol
calculation. Based on 492 interproton and 10 hydrogen-bonding distance
restraints and 36 dihedral angle restraints, we obtained 20 structures. The
average backbone root-mean-square deviation for residues 4-35 is 0.728 +/- 0.217
A from the mean structure. The solution structure consists of a two-stranded
antiparallel beta-sheet connected by a type-I beta-turn after a short helical
turn. All secondary structures and a conserved disulfide bond are located in the
C-terminal half of the peptide, residues 18-36. Overall folding is stabilized by
a combination of a disulfide bond, seven hydrogen bonds, and numerous
hydrophobic interactions. The structural motif of the C-terminal half shares a
significant tertiary structural similarity with chitin-binding domains of plant
and invertebrate chitin-binding proteins, even though scarabaecin has no overall
sequence similarity to other peptide/polypeptides including chitin-binding
proteins. The length of its primary structure, the number of disulfide bonds,
and the pattern of conserved functional residues binding to chitin in
scarabaecin differ from those of chitin-binding proteins in other invertebrates
and plants, suggesting that scarabaecin does not share a common ancestor with
them. These results are thought to provide further strong experimental evidence
to the hypothesis that chitin-binding proteins of invertebrates and plants are
correlated by a convergent evolution process.
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Figure 3.
FIG. 3. A, superimposition of 20 selected structures of
scarabaecin with lowest total energy, calculated by means of the
hybrid distance geometry-simulated annealing procedure of X-PLOR
3.851 (31). B, schematic ribbon drawing of the restrained
minimized average structure of scarabaecin. Scarabaecin is shown
with the  -sheet in front.
Disulfide bridges are shown as ball-and-stick models. C,
scarabaecin is rotated by 180° about the vertical axis.
Nonhydrogen side chain atoms of the residues forming hydrophobic
interaction are shown.
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Figure 4.
FIG. 4. Comparison of the structure of the putative
chitinbinding region in scarabaecin (Cys-18-Ser-36) with that in
tachycitin (Cys-40-Gly-60) and the structure of the previously
identified chitin-binding region in hevein (Cys-12-Ser-32).
Backbone atoms of residues 18-30 (scarabaecin, blue); 40-49,
52-54 (tachycitin, red); and 12-21, 23-25 (hevein, green) were
used for superposition. The side chains of the conserved
cysteine and putative or really functional residues of all three
structures are shown, with cysteine sulfur atoms colored yellow.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
22820-22827)
copyright 2003.
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