2dkv - Revision history

OCA at 05:10, 17 October 2024

2024-10-17T05:10:10Z

← Older revision		Revision as of 05:10, 17 October 2024
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	<StructureSection load='2dkv' size='340' side='right'caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2dkv' size='340' side='right'caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Japanese_rice Japanese rice~~]. 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>		<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>
	</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>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </span></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='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>		<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>
	</table>		</table>
			== Function ==
			[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]]
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkv_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkv_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Chitinase]]~~
	~~[[Category: Japanese rice]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Kezuka, Y~~]]		[[Category: Oryza sativa Japonica Group]]
	[[Category: ~~Nishizawa,~~ Y]]		[[Category: Kezuka Y]]
	[[Category: ~~Nonaka, T~~]]		[[Category: Nishizawa Y]]
	[[Category: ~~Watanabe,~~ T]]		[[Category: Nonaka T]]
	[[Category: ~~Class i chitinase]]~~		[[Category: Watanabe T]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Oryza sativa l. japonica]]~~
	~~[[Category: Whole structure~~]]

OCA at 20:38, 20 October 2021

2021-10-20T20:38:07Z

← Older revision		Revision as of 20:38, 20 October 2021
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	<StructureSection load='2dkv' size='340' side='right'caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2dkv' size='340' side='right'caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkv]] is a 1 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=2DKV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DKV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. 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>
	</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='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='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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [https://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=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [~~http~~://pdbe.org/2dkv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dkv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkv 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=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>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:32, 1 January 2020

2020-01-01T08:32:42Z

← Older revision		Revision as of 08:32, 1 January 2020
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	==Crystal structure of class I chitinase from Oryza sativa L. japonica==		==Crystal structure of class I chitinase from Oryza sativa L. japonica==
	<StructureSection load='2dkv' size='340' side='right' caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2dkv' size='340' side='right'caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkv]] is a 1 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=2DKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkv]] is a 1 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=2DKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKV FirstGlance]. <br>
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	~~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~~.		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.

	~~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:~~7901749~~<ref>PMID:~~7901749~~</ref>		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>

	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>
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	==See Also==		==See Also==
	*[[Chitinase\|Chitinase]]		*[[Chitinase 3D structures\|Chitinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Chitinase]]		[[Category: Chitinase]]
	[[Category: Japanese rice]]		[[Category: Japanese rice]]
			[[Category: Large Structures]]
	[[Category: Kezuka, Y]]		[[Category: Kezuka, Y]]
	[[Category: Nishizawa, Y]]		[[Category: Nishizawa, Y]]

OCA at 06:22, 30 May 2018

2018-05-30T06:22:19Z

← Older revision		Revision as of 06:22, 30 May 2018
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	==Crystal structure of class I chitinase from Oryza sativa L. japonica==		==Crystal structure of class I chitinase from Oryza sativa L. japonica==
	<StructureSection load='2dkv' size='340' side='right' caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2dkv' size='340' side='right' caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	</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='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>
	<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='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=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [http://pdbe.org/2dkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum]</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=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [http://pdbe.org/2dkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkv_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkv_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>

OCA at 14:51, 9 February 2016

2016-02-09T14:51:40Z

← Older revision		Revision as of 14:51, 9 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</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].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:19, 10 September 2015

2015-09-10T23:19:14Z

← Older revision		Revision as of 23:19, 10 September 2015
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	<StructureSection load='2dkv' size='340' side='right' caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2dkv' size='340' side='right' caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkv]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkv]] is a 1 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=2DKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKV 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='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>
	<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='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=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum]</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=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [http://pdbe.org/2dkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2dkv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Chitinase]]		[[Category: Chitinase]]
	[[Category: ~~Oryza sativa japonica group~~]]		[[Category: Japanese rice]]
	[[Category: Kezuka, Y]]		[[Category: Kezuka, Y]]
	[[Category: Nishizawa, Y]]		[[Category: Nishizawa, Y]]

OCA at 17:47, 15 January 2015

2015-01-15T17:47:17Z

← Older revision		Revision as of 17:47, 15 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkv]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkv]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKV FirstGlance]. <br>
	</td></tr><tr><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><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>
	<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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum]</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=2dkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Chitinase]]		[[Category: Chitinase]]
	[[Category: Oryza sativa japonica group]]		[[Category: Oryza sativa japonica group]]
	[[Category: Kezuka, Y.]]		[[Category: Kezuka, Y]]
	[[Category: Nishizawa, Y.]]		[[Category: Nishizawa, Y]]
	[[Category: Nonaka, T.]]		[[Category: Nonaka, T]]
	[[Category: Watanabe, T.]]		[[Category: Watanabe, T]]
	[[Category: Class i chitinase]]		[[Category: Class i chitinase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Oryza sativa l. japonica]]		[[Category: Oryza sativa l. japonica]]
	[[Category: Whole structure]]		[[Category: Whole structure]]

OCA at 02:54, 29 September 2014

2014-09-29T02:54:51Z

← Older revision		Revision as of 02:54, 29 September 2014
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	[[Image:~~2dkv~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of class I chitinase from Oryza sativa L. japonica==
			<StructureSection load='2dkv' size='340' side='right' caption='[[2dkv]], [[Resolution\|resolution]] 2.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dkv]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKV FirstGlance]. <br>
			</td></tr><tr><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><br>
			<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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=2dkv RCSB], [http://www.ebi.ac.uk/pdbsum/2dkv PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkv_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</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/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			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.

	~~{{STRUCTURE_2dkv\| PDB=2dkv \| SCENE= }}~~		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:7901749<ref>PMID:7901749</ref>

	~~===Crystal structure~~ of ~~class I chitinase from Oryza sativa L~~. ~~japonica===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_7901749}}~~

	~~==About this Structure==~~
	~~[[2dkv]] is a 1 chain structure with sequence from [http://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].~~

	==See Also==		==See Also==
	*[[Chitinase\|Chitinase]]		*[[Chitinase\|Chitinase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:007901749<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Chitinase]]		[[Category: Chitinase]]
	[[Category: Oryza sativa japonica group]]		[[Category: Oryza sativa japonica group]]

OCA at 14:12, 20 October 2012

2012-10-20T14:12:43Z

← Older revision		Revision as of 14:12, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2dkv]] is a 1 chain structure ~~of [[Chitinase]]~~ with sequence from [http://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].		[[2dkv]] is a 1 chain structure with sequence from [http://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].

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
	<ref group="xtra">PMID:007901749~~</ref><ref group="xtra">PMID:015327374~~</ref><references group="xtra"/>		<ref group="xtra">PMID:007901749</ref><references group="xtra"/>
	[[Category: Chitinase]]		[[Category: Chitinase]]
	[[Category: Oryza sativa japonica group]]		[[Category: Oryza sativa japonica group]]

OCA at 14:25, 26 July 2012

2012-07-26T14:25:30Z

← Older revision		Revision as of 14:25, 26 July 2012
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	[[Image:2dkv.png\|left\|200px]]		[[Image:2dkv.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dkv", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2dkv\| PDB=2dkv \| SCENE= }}		{{STRUCTURE_2dkv\| PDB=2dkv \| SCENE= }}

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


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_7901749}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 7901749 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_7901749}}		{{ABSTRACT_PUBMED_7901749}}

	==About this Structure==		==About this Structure==
	[[2dkv]] is a 1 chain structure with sequence from [http://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].		[[2dkv]] is a 1 chain structure of [[Chitinase]] with sequence from [http://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].

			==See Also==
			*[[Chitinase\|Chitinase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~7901749~~</ref><ref group="xtra">PMID:~~15327374~~</ref><references group="xtra"/>		<ref group="xtra">PMID:007901749</ref><ref group="xtra">PMID:015327374</ref><references group="xtra"/>
	[[Category: Chitinase]]		[[Category: Chitinase]]
	[[Category: Oryza sativa japonica group]]		[[Category: Oryza sativa japonica group]]