6idn
From Proteopedia
(Difference between revisions)
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<StructureSection load='6idn' size='340' side='right'caption='[[6idn]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='6idn' size='340' side='right'caption='[[6idn]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'> | + | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IDN FirstGlance]. <br> |
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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=6idn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idn OCA], [https://pdbe.org/6idn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6idn RCSB], [https://www.ebi.ac.uk/pdbsum/6idn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6idn ProSAT]</span></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=6idn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idn OCA], [https://pdbe.org/6idn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6idn RCSB], [https://www.ebi.ac.uk/pdbsum/6idn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6idn ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| - | == Function == | ||
| - | [https://www.uniprot.org/uniprot/A0A493R6X2_9ASTE A0A493R6X2_9ASTE] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The ICChI is a 35-kDa, glycosylated protein isolated from the latex of the weed Ipomoea carnea. It displays chitinase and lysozyme activity, which could be important for the defense against pathogenic fungi, insects and bacteria. The ICChI enzyme was crystallized, and a diffraction data set was collected from a single crystal to 1.42 A resolution. The crystals belong to the primitive tetragonal space group P43212, with unit-cell parameters a = b = 57.9, c = 172.0 A, and alpha = beta = gamma = 90 degrees . The structure was elucidated by molecular replacement method using a mixed model of three homologous structures from the N-terminal sequence of ICChI. The refined model consists of 272 amino acid residues and has a Rfactor of 18.93% and Rfree of 22.42%. The protein consists of a single globular domain with a (alpha/beta)8 triosephosphate isomerase barrel fold. Three of the consensus sites for N-glycosylation viz., Asn(45), Asn(172), and Asn(194) containing carbohydrate moieties N-Acetylglucosamine (NAG), mannose, fucose, and xylose. The putative catalytic residues are Asp(125), Glu(127), and Tyr(184). The crystal structure may provide fundamental information of GH18 family chitinases. | ||
| - | |||
| - | TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity.,Kumar S, Kumar A, Patel AK Phytochemistry. 2020 Feb;170:112221. doi: 10.1016/j.phytochem.2019.112221. Epub, 2019 Nov 29. PMID:31790908<ref>PMID:31790908</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 6idn" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Chitinase 3D structures|Chitinase 3D structures]] | *[[Chitinase 3D structures|Chitinase 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Ipomoea carnea]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Kumar A]] | [[Category: Kumar A]] | ||
[[Category: Kumar S]] | [[Category: Kumar S]] | ||
[[Category: Patel AK]] | [[Category: Patel AK]] | ||
Current revision
Crystal structure of ICChI chitinase from ipomoea carnea
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