2dkv

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[[Image:2dkv.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of class I chitinase from Oryza sativa L. japonica==
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|PDB= 2dkv |SIZE=350|CAPTION= <scene name='initialview01'>2dkv</scene>, resolution 2.00&Aring;
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<StructureSection load='2dkv' size='340' side='right'caption='[[2dkv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
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<table><tr><td colspan='2'>[[2dkv]] is a 1 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=2DKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKV FirstGlance]. <br>
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|ACTIVITY= <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>
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</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&#8491;</td></tr>
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|GENE=
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<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>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [https://pdbe.org/2dkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [https://www.ebi.ac.uk/pdbsum/2dkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkv ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB]</span>
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== Function ==
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}}
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkv_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dkv ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal structure of class I chitinase from Oryza sativa L. japonica'''
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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<ref>PMID:20544965</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2dkv" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Rice chitinases are encoded by a small multigene family. To clarify the overall organization of rice chitinase genes, we have isolated and characterized the genes Cht-1, Cht-2 and Cht-3. Although all the three genes encode class I chitinase, the nucleotide sequences of the coding regions of Cht-1 and Cht-3 are very similar (90%), while that of Cht-2 is clearly more divergent (78%). Only Cht-2 has a 130 bp intron and encodes a C-terminal peptide sequence similar to that known to function as a vacuolar targeting signal. In 5' flanking regions of Cht-1 and Cht-3, but not of Cht-2, conserved sequences (GGCCGGCYGCCCYAG) were found. Related sequences were found also in the 5' flanking regions of another chitinase gene and a beta-glucanase gene which has also been reported to be stress-induced in rice. RNA blot hybridization analysis demonstrated that the stress-induced expression patterns of the Cht-1 and Cht-3 genes are similar, but quite different from that of Cht-2. However, all three genes are active in unstressed roots. By restriction fragment length polymorphism (RFLP) linkage analysis, Cht-1 and Cht-3 were mapped onto chromosome 6 and shown to be closely linked (0.8 cM). Cht-2 was mapped onto chromosome 5. All these features suggest that the expression patterns of rice class I chitinase genes may be correlated with their levels of sequence divergence and their chromosomal location.
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*[[Chitinase 3D structures|Chitinase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2DKV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKV OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Sequence variation, differential expression and chromosomal location of rice chitinase genes., Nishizawa Y, Kishimoto N, Saito A, Hibi T, Mol Gen Genet. 1993 Oct;241(1-2):1-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7901749 7901749]
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[[Category: Oryza sativa Japonica Group]]
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[[Category: Chitinase]]
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[[Category: Kezuka Y]]
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[[Category: Oryza sativa]]
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[[Category: Nishizawa Y]]
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[[Category: Single protein]]
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[[Category: Nonaka T]]
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[[Category: Kezuka, Y.]]
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[[Category: Watanabe T]]
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[[Category: Nishizawa, Y.]]
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[[Category: Nonaka, T.]]
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[[Category: Watanabe, T.]]
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[[Category: class i chitinase]]
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[[Category: oryza sativa l. japonica]]
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[[Category: whole structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:35:58 2008''
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Current revision

Crystal structure of class I chitinase from Oryza sativa L. japonica

PDB ID 2dkv

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