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| | ==Crystal structure of a class V chitinase from Arabidopsis thaliana== | | ==Crystal structure of a class V chitinase from Arabidopsis thaliana== |
| - | <StructureSection load='3aqu' size='340' side='right' caption='[[3aqu]], [[Resolution|resolution]] 2.01Å' scene=''> | + | <StructureSection load='3aqu' size='340' side='right'caption='[[3aqu]], [[Resolution|resolution]] 2.01Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3aqu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AQU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3aqu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AQU FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene><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]] 2.01Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT4g19810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </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=3aqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aqu OCA], [https://pdbe.org/3aqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aqu RCSB], [https://www.ebi.ac.uk/pdbsum/3aqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aqu ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3aqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aqu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3aqu RCSB], [http://www.ebi.ac.uk/pdbsum/3aqu PDBsum]</span></td></tr> | + | </table> |
| - | <table> | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/CHIC_ARATH CHIC_ARATH] Can hydrolyze glycol chitin and chitin oligosaccharides (e.g. N-acetylglucosamine) (GlcNAc)4, (GlcNAc)5 and (GlcNAc)6 (PubMed:21390509, PubMed:22936594). Hydrolyzes N-acetylglucosamine oligomers producing dimers from the non-reducing end of the substrates (PubMed:21390509).<ref>PMID:21390509</ref> <ref>PMID:22936594</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis.,Ohnuma T, Numata T, Osawa T, Mizuhara M, Lampela O, Juffer AH, Skriver K, Fukamizo T Planta. 2011 Jul;234(1):123-37. Epub 2011 Mar 9. PMID:21390509<ref>PMID:21390509</ref> | | A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis.,Ohnuma T, Numata T, Osawa T, Mizuhara M, Lampela O, Juffer AH, Skriver K, Fukamizo T Planta. 2011 Jul;234(1):123-37. Epub 2011 Mar 9. PMID:21390509<ref>PMID:21390509</ref> |
| | | | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3aqu" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Arabidopsis thaliana]] | | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Chitinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Fukamizo, T.]] | + | [[Category: Fukamizo T]] |
| - | [[Category: Numata, T.]] | + | [[Category: Numata T]] |
| - | [[Category: Ohnuma, T.]] | + | [[Category: Ohnuma T]] |
| - | [[Category: Osawa, T.]] | + | [[Category: Osawa T]] |
| - | [[Category: Chitin]]
| + | |
| - | [[Category: Hydrolase]]
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| - | [[Category: Stress response]]
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| - | [[Category: Tim barrel]]
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| Structural highlights
Function
CHIC_ARATH Can hydrolyze glycol chitin and chitin oligosaccharides (e.g. N-acetylglucosamine) (GlcNAc)4, (GlcNAc)5 and (GlcNAc)6 (PubMed:21390509, PubMed:22936594). Hydrolyzes N-acetylglucosamine oligomers producing dimers from the non-reducing end of the substrates (PubMed:21390509).[1] [2]
Publication Abstract from PubMed
Expression of a class V chitinase gene (At4g19810, AtChiC) in Arabidopsis thaliana was examined by quantitative real-time PCR and by analyzing microarray data available at Genevestigator. The gene expression was induced by the plant stress-related hormones abscisic acid (ABA) and jasmonic acid (JA) and by the stress resulting from the elicitor flagellin, NaCl, and osmosis. The recombinant AtChiC protein was produced in E. coli, purified, and characterized with respect to the structure and function. The recombinant AtChiC hydrolyzed N-acetylglucosamine oligomers producing dimers from the non-reducing end of the substrates. The crystal structure of AtChiC was determined by the molecular replacement method at 2.0 A resolution. AtChiC was found to adopt an (beta/alpha)(8) fold with a small insertion domain composed of an alpha-helix and a five-stranded beta-sheet. From docking simulation of AtChiC with pentameric substrate, the amino acid residues responsible for substrate binding were found to be well conserved when compared with those of the class V chitinase from Nicotiana tabacum (NtChiV). All of the structural and functional properties of AtChiC are quite similar to those obtained for NtChiV, and seem to be common to class V chitinases from higher plants.
A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis.,Ohnuma T, Numata T, Osawa T, Mizuhara M, Lampela O, Juffer AH, Skriver K, Fukamizo T Planta. 2011 Jul;234(1):123-37. Epub 2011 Mar 9. PMID:21390509[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ohnuma T, Numata T, Osawa T, Mizuhara M, Lampela O, Juffer AH, Skriver K, Fukamizo T. A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis. Planta. 2011 Jul;234(1):123-37. Epub 2011 Mar 9. PMID:21390509 doi:10.1007/s00425-011-1390-3
- ↑ Umemoto N, Ohnuma T, Mizuhara M, Sato H, Skriver K, Fukamizo T. Introduction of a tryptophan side chain into subsite +1 enhances transglycosylation activity of a GH-18 chitinase from Arabidopsis thaliana, AtChiC. Glycobiology. 2013 Jan;23(1):81-90. PMID:22936594 doi:10.1093/glycob/cws125
- ↑ Ohnuma T, Numata T, Osawa T, Mizuhara M, Lampela O, Juffer AH, Skriver K, Fukamizo T. A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis. Planta. 2011 Jul;234(1):123-37. Epub 2011 Mar 9. PMID:21390509 doi:10.1007/s00425-011-1390-3
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