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| - | {{Seed}} | |
| - | [[Image:1iyc.png|left|200px]] | |
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| - | <!-- | + | ==Solution structure of antifungal peptide, scarabaecin== |
| - | The line below this paragraph, containing "STRUCTURE_1iyc", creates the "Structure Box" on the page.
| + | <StructureSection load='1iyc' size='340' side='right'caption='[[1iyc]]' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1iyc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctes_rhinoceros Oryctes rhinoceros]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IYC FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | --> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyc OCA], [https://pdbe.org/1iyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iyc RCSB], [https://www.ebi.ac.uk/pdbsum/1iyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iyc ProSAT]</span></td></tr> |
| - | {{STRUCTURE_1iyc| PDB=1iyc | SCENE= }}
| + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SCAB_ORYRH SCAB_ORYRH] Possesses antifungal activity against phytopathogenic fungi such as P.oryzae, R.solani and B.cinerea but not against phytopathogenic bacteria. Shows weak activity against the insect pathogenic fungus B.bassiana and against S.aureus. Binds chitin.<ref>PMID:12859949</ref> <ref>PMID:12676931</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | 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. |
| | | | |
| - | ===Solution structure of antifungal peptide, scarabaecin===
| + | 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.,Hemmi H, Ishibashi J, Tomie T, Yamakawa M J Biol Chem. 2003 Jun 20;278(25):22820-7. Epub 2003 Apr 3. PMID:12676931<ref>PMID:12676931</ref> |
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| - | | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | <!--
| + | </div> |
| - | The line below this paragraph, {{ABSTRACT_PUBMED_12676931}}, adds the Publication Abstract to the page
| + | <div class="pdbe-citations 1iyc" style="background-color:#fffaf0;"></div> |
| - | (as it appears on PubMed at http://www.pubmed.gov), where 12676931 is the PubMed ID number.
| + | == References == |
| - | --> | + | <references/> |
| - | {{ABSTRACT_PUBMED_12676931}}
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==About this Structure== | + | [[Category: Large Structures]] |
| - | 1IYC is a [[Single protein]] structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYC OCA].
| + | [[Category: Oryctes rhinoceros]] |
| - | | + | [[Category: Hemmi H]] |
| - | ==Reference==
| + | [[Category: Ishibashi J]] |
| - | 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., Hemmi H, Ishibashi J, Tomie T, Yamakawa M, J Biol Chem. 2003 Jun 20;278(25):22820-7. Epub 2003 Apr 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12676931 12676931]
| + | [[Category: Tomie T]] |
| - | [[Category: Single protein]] | + | [[Category: Yamakawa M]] |
| - | [[Category: Hemmi, H.]] | + | |
| - | [[Category: Ishibashi, J.]] | + | |
| - | [[Category: Tomie, T.]] | + | |
| - | [[Category: Yamakawa, M.]] | + | |
| - | [[Category: Antifungal peptide]]
| + | |
| - | [[Category: Antimicrobial peptide]]
| + | |
| - | [[Category: Beetle]]
| + | |
| - | [[Category: Chitin-binding]]
| + | |
| - | [[Category: Nmr]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 14:12:54 2008''
| + | |
| Structural highlights
Function
SCAB_ORYRH Possesses antifungal activity against phytopathogenic fungi such as P.oryzae, R.solani and B.cinerea but not against phytopathogenic bacteria. Shows weak activity against the insect pathogenic fungus B.bassiana and against S.aureus. Binds chitin.[1] [2]
Publication Abstract from PubMed
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.
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.,Hemmi H, Ishibashi J, Tomie T, Yamakawa M J Biol Chem. 2003 Jun 20;278(25):22820-7. Epub 2003 Apr 3. PMID:12676931[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tomie T, Ishibashi J, Furukawa S, Kobayashi S, Sawahata R, Asaoka A, Tagawa M, Yamakawa M. Scarabaecin, a novel cysteine-containing antifungal peptide from the rhinoceros beetle, Oryctes rhinoceros. Biochem Biophys Res Commun. 2003 Jul 25;307(2):261-6. PMID:12859949
- ↑ Hemmi H, Ishibashi J, Tomie T, Yamakawa M. 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. 2003 Jun 20;278(25):22820-7. Epub 2003 Apr 3. PMID:12676931 doi:10.1074/jbc.M301025200
- ↑ Hemmi H, Ishibashi J, Tomie T, Yamakawa M. 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. 2003 Jun 20;278(25):22820-7. Epub 2003 Apr 3. PMID:12676931 doi:10.1074/jbc.M301025200
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