spacer
spacer

PDBsum entry 1iyc

Go to PDB code: 
protein links
Antifungal protein PDB id
1iyc
Jmol
Contents
Protein chain
36 a.a.
PDB id:
1iyc
Name: Antifungal protein
Title: Solution structure of antifungal peptide, scarabaecin
Structure: Scarabaecin. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence occurs naturally in the coconut rhinoceros beetle.
NMR struc: 20 models
Authors: H.Hemmi,J.Ishibashi,T.Tomie,M.Yamakawa
Key ref:
H.Hemmi et al. (2003). 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. J Biol Chem, 278, 22820-22827. PubMed id: 12676931 DOI: 10.1074/jbc.M301025200
Date:
05-Aug-02     Release date:   24-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q86SC0  (SCAB_ORYRH) -  Scarabaecin
Seq:
Struc:
66 a.a.
36 a.a.
Key:    PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     killing of cells of other organism   4 terms 
  Biochemical function     chitin binding     1 term  

 

 
DOI no: 10.1074/jbc.M301025200 J Biol Chem 278:22820-22827 (2003)
PubMed id: 12676931  
 
 
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.
H.Hemmi, J.Ishibashi, T.Tomie, M.Yamakawa.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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.
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.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 22820-22827) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17641929 W.Loongyai, J.C.Avarre, M.Cerutti, E.Lubzens, and W.Chotigeat (2007).
Isolation and functional characterization of a new shrimp ovarian peritrophin with antimicrobial activity from Fenneropenaeus merguiensis.
  Mar Biotechnol (NY), 9, 624-637.  
15199961 E.Bachère, Y.Gueguen, M.Gonzalez, J.de Lorgeril, J.Garnier, and B.Romestand (2004).
Insights into the anti-microbial defense of marine invertebrates: the penaeid shrimps and the oyster Crassostrea gigas.
  Immunol Rev, 198, 149-168.  
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.