|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of class I chitinase from Oryza sativa L. japonica== | | ==Crystal structure of class I chitinase from Oryza sativa L. japonica== |
| - | <StructureSection load='3iwr' size='340' side='right' caption='[[3iwr]], [[Resolution|resolution]] 2.57Å' scene=''> | + | <StructureSection load='3iwr' size='340' side='right'caption='[[3iwr]], [[Resolution|resolution]] 2.57Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3iwr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IWR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3iwr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IWR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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]] 2.57Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dkv|2dkv]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cht-2, OsJ_18467 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=3iwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwr OCA], [https://pdbe.org/3iwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iwr RCSB], [https://www.ebi.ac.uk/pdbsum/3iwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwr ProSAT]</span></td></tr> |
| - | <tr id='activity'><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3iwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwr OCA], [http://pdbe.org/3iwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iwr RCSB], [http://www.ebi.ac.uk/pdbsum/3iwr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CHI2_ORYSJ CHI2_ORYSJ]] Hydrolyzes chitin and plays a role in defense against fungal pathogens containing chitin. Its overexpression confers enhanced resistance to sheath blight pathogen (R.solani).<ref>PMID:11166426</ref> <ref>PMID:18211919</ref> <ref>PMID:18323646</ref> | + | [https://www.uniprot.org/uniprot/CHI2_ORYSJ CHI2_ORYSJ] Hydrolyzes chitin and plays a role in defense against fungal pathogens containing chitin. Its overexpression confers enhanced resistance to sheath blight pathogen (R.solani).<ref>PMID:11166426</ref> <ref>PMID:18211919</ref> <ref>PMID:18323646</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iw/3iwr_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iw/3iwr_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| Line 33: |
Line 31: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Chitinase|Chitinase]] | + | *[[Chitinase 3D structures|Chitinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chitinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Japanese rice]] | + | [[Category: Oryza sativa Japonica Group]] |
| - | [[Category: Kezuka, Y]] | + | [[Category: Kezuka Y]] |
| - | [[Category: Nonaka, T]] | + | [[Category: Nonaka T]] |
| - | [[Category: Watanabe, T]] | + | [[Category: Watanabe T]] |
| - | [[Category: Chitin-binding]]
| + | |
| - | [[Category: Class i chitinase]]
| + | |
| - | [[Category: Glycosidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Oryza sativa l. japonica]]
| + | |
| Structural highlights
Function
CHI2_ORYSJ Hydrolyzes chitin and plays a role in defense against fungal pathogens containing chitin. Its overexpression confers enhanced resistance to sheath blight pathogen (R.solani).[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The rice class I chitinase OsChia1b, also referred to as RCC2 or Cht-2, is composed of an N-terminal chitin-binding domain (ChBD) and a C-terminal catalytic domain (CatD), which are connected by a proline- and threonine-rich linker peptide. Because of the ability to inhibit fungal growth, the OsChia1b gene has been used to produce transgenic plants with enhanced disease resistance. As an initial step toward elucidating the mechanism of hydrolytic action and antifungal activity, the full-length structure of OsChia1b was analyzed by X-ray crystallography and small-angle X-ray scattering (SAXS). We determined the crystal structure of full-length OsChia1b at 2.00-A resolution, but there are two possibilities for a biological molecule with and without interdomain contacts. The SAXS data showed an extended structure of OsChia1b in solution compared to that in the crystal form. This extension could be caused by the conformational flexibility of the linker. A docking simulation of ChBD with tri-N-acetylchitotriose exhibited a similar binding mode to the one observed in the crystal structure of a two-domain plant lectin complexed with a chitooligosaccharide. A hypothetical model based on the binding mode suggested that ChBD is unsuitable for binding to crystalline alpha-chitin, which is a major component of fungal cell walls because of its collisions with the chitin chains on the flat surface of alpha-chitin. This model also indicates the difference in the binding specificity of plant and bacterial ChBDs of GH19 chitinases, which contribute to antifungal activity.
Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.,Kezuka Y, Kojima M, Mizuno R, Suzuki K, Watanabe T, Nonaka T Proteins. 2010 Aug 1;78(10):2295-305. PMID:20544965[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Datta K, Tu J, Oliva N, Ona I I, Velazhahan R, Mew TW, Muthukrishnan S, Datta SK. Enhanced resistance to sheath blight by constitutive expression of infection-related rice chitinase in transgenic elite indica rice cultivars. Plant Sci. 2001 Feb 5;160(3):405-414. PMID:11166426
- ↑ Mizuno R, Fukamizo T, Sugiyama S, Nishizawa Y, Kezuka Y, Nonaka T, Suzuki K, Watanabe T. Role of the loop structure of the catalytic domain in rice class I chitinase. J Biochem. 2008 Apr;143(4):487-95. doi: 10.1093/jb/mvn004. Epub 2008 Jan 22. PMID:18211919 doi:http://dx.doi.org/10.1093/jb/mvn004
- ↑ Mizuno R, Itoh Y, Nishizawa Y, Kezuka Y, Suzuki K, Nonaka T, Watanabe T. Purification and characterization of a rice class I chitinase, OsChia1b, produced in Esherichia coli. Biosci Biotechnol Biochem. 2008 Mar;72(3):893-5. Epub 2008 Mar 7. PMID:18323646 doi:http://dx.doi.org/10.1271/bbb.70693
- ↑ Kezuka Y, Kojima M, Mizuno R, Suzuki K, Watanabe T, Nonaka T. Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Proteins. 2010 Aug 1;78(10):2295-305. PMID:20544965 doi:10.1002/prot.22742
|
