1j0m - Revision history

OCA at 23:40, 27 December 2023

2023-12-27T23:40:12Z

←Older revision		Revision as of 23:40, 27 December 2023
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	<StructureSection load='1j0m' size='340' side='right'caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1j0m' size='340' side='right'caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacgl Bacgl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1J0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._GL1 Bacillus sp. GL1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J0M FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1j0n\|1j0n]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~84635 BACGL])</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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [https://pdbe.org/1j0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [https://www.ebi.ac.uk/pdbsum/1j0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0m 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/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [~~http~~://pdbe.org/1j0m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1j0m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0m ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/XANLY_BACGL XANLY_BACGL]] Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.<ref>PMID:10347037</ref> <ref>PMID:11157235</ref> <ref>PMID:9758797</ref>	+	[https://www.uniprot.org/uniprot/XANLY_BACGL XANLY_BACGL] Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.<ref>PMID:10347037</ref> <ref>PMID:11157235</ref> <ref>PMID:9758797</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacgl~~]]	+	[[Category: Bacillus sp. GL1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Xanthan lyase]]~~	+	[[Category: Hashimoto W]]
-	[[Category: Hashimoto, W]]	+	[[Category: Mikami B]]
-	[[Category: Mikami, B]]	+	[[Category: Murata K]]
-	[[Category: Murata, K]]	+	[[Category: Nankai H]]
-	[[Category: Nankai, H]]	+
-	~~[[Category: Alpha/alpha barrel]]~~	+
-	~~[[Category: Anti-parallel beta-sheet]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 07:26, 25 November 2020

2020-11-25T07:26:46Z

←Older revision		Revision as of 07:26, 25 November 2020
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	==Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan==		==Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan==
-	<StructureSection load='1j0m' size='340' side='right' caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1j0m' size='340' side='right'caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacgl Bacgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1J0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacgl Bacgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1J0M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j0n\|1j0n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j0n\|1j0n]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84635 BACGL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84635 BACGL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://pdbe.org/1j0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0m ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://pdbe.org/1j0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j0/1j0m_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j0/1j0m_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 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bacgl]]		[[Category: Bacgl]]
		+	[[Category: Large Structures]]
	[[Category: Xanthan lyase]]		[[Category: Xanthan lyase]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]

OCA at 09:56, 4 October 2017

2017-10-04T09:56:04Z

←Older revision		Revision as of 09:56, 4 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan==		==Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan==
	<StructureSection load='1j0m' size='340' side='right' caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1j0m' size='340' side='right' caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84635 BACGL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84635 BACGL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://pdbe.org/1j0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m 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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://pdbe.org/1j0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=1j0m ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:12, 11 September 2015

2015-09-11T09:12:25Z

←Older revision		Revision as of 09:12, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1j0m' size='340' side='right' caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1j0m' size='340' side='right' caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_sp. Bacillus sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacgl Bacgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J0M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j0n\|1j0n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j0n\|1j0n]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1409 Bacillus sp.~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84635 BACGL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m 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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://pdbe.org/1j0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/XANLY_BACGL XANLY_BACGL]] Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.<ref>PMID:10347037</ref> <ref>PMID:11157235</ref> <ref>PMID:9758797</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 29:
	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 1j0m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus sp~~]]	+	[[Category: Bacgl]]
	[[Category: Xanthan lyase]]		[[Category: Xanthan lyase]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]

OCA at 12:22, 2 January 2015

2015-01-02T12:22:41Z

←Older revision		Revision as of 12:22, 2 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J0M FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J0M FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j0n\|1j0n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j0n\|1j0n]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1409 Bacillus sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1409 Bacillus sp.])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m 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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus sp.]]	+	[[Category: Bacillus sp]]
	[[Category: Xanthan lyase]]		[[Category: Xanthan lyase]]
-	[[Category: Hashimoto, W.]]	+	[[Category: Hashimoto, W]]
-	[[Category: Mikami, B.]]	+	[[Category: Mikami, B]]
-	[[Category: Murata, K.]]	+	[[Category: Murata, K]]
-	[[Category: Nankai, H.]]	+	[[Category: Nankai, H]]
	[[Category: Alpha/alpha barrel]]		[[Category: Alpha/alpha barrel]]
	[[Category: Anti-parallel beta-sheet]]		[[Category: Anti-parallel beta-sheet]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 13:20, 28 September 2014

2014-09-28T13:20:40Z

←Older revision		Revision as of 13:20, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1j0m.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan==
		+	<StructureSection load='1j0m' size='340' side='right' caption='[[1j0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J0M FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j0n\|1j0n]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XLY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1409 Bacillus sp.])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=1j0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j0m RCSB], [http://www.ebi.ac.uk/pdbsum/1j0m 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/j0/1j0m_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 ==
		+	Xanthan lyase, a member of polysaccharide lyase family 8, is a key enzyme for complete depolymerization of a bacterial heteropolysaccharide, xanthan, in Bacillus sp. GL1. The enzyme acts exolytically on the side chains of the polysaccharide. The x-ray crystallographic structure of xanthan lyase was determined by the multiple isomorphous replacement method. The crystal structures of xanthan lyase and its complex with the product (pyruvylated mannose) were refined at 2.3 and 2.4 A resolution with final R-factors of 17.5 and 16.9%, respectively. The refined structure of the product-free enzyme comprises 752 amino acid residues, 248 water molecules, and one calcium ion. The enzyme consists of N-terminal alpha-helical and C-terminal beta-sheet domains, which constitute incomplete alpha(5)/alpha(5)-barrel and anti-parallel beta-sheet structures, respectively. A deep cleft is located in the N-terminal alpha-helical domain facing the interface between the two domains. Although the overall structure of the enzyme is basically the same as that of the family 8 lyases for hyaluronate and chondroitin AC, significant differences were observed in the loop structure over the cleft. The crystal structure of the xanthan lyase complexed with pyruvylated mannose indicates that the sugar-binding site is located in the deep cleft, where aromatic and positively charged amino acid residues are involved in the binding. The Arg(313) and Tyr(315) residues in the loop from the N-terminal domain and the Arg(612) residue in the loop from the C-terminal domain directly bind to the pyruvate moiety of the product through the formation of hydrogen bonds, thus determining the substrate specificity of the enzyme.

-	~~{{STRUCTURE_1j0m\| PDB=1j0m \| SCENE= }}~~	+	Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.,Hashimoto W, Nankai H, Mikami B, Murata K J Biol Chem. 2003 Feb 28;278(9):7663-73. Epub 2002 Dec 9. PMID:12475987<ref>PMID:12475987</ref>

-	~~===Crystal Structure~~ of ~~Bacillus sp~~. ~~GL1 Xanthan Lyase that Acts on Side Chains~~ of ~~Xanthan===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12475987}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1j0m]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012475987<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
	[[Category: Xanthan lyase]]		[[Category: Xanthan lyase]]

OCA: Protected "1j0m" [edit=sysop:move=sysop]

2012-11-28T15:12:28Z

Protected "1j0m" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:12, 28 November 2012

OCA at 15:12, 28 November 2012

2012-11-28T15:12:26Z

←Older revision		Revision as of 15:12, 28 November 2012
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-	{{Seed}}
	[[Image:1j0m.png\|left\|200px]]		[[Image:1j0m.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1j0m", 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_1j0m\| PDB=1j0m \| SCENE= }}		{{STRUCTURE_1j0m\| PDB=1j0m \| SCENE= }}

	===Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan===		===Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12475987}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12475987 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12475987}}		{{ABSTRACT_PUBMED_12475987}}

	==About this Structure==		==About this Structure==
-	~~1J0M~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA].	+	[[1j0m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12475987~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012475987</ref><references group="xtra"/>
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
	[[Category: Xanthan lyase]]		[[Category: Xanthan lyase]]
Line 32:		Line 20:
	[[Category: Alpha/alpha barrel]]		[[Category: Alpha/alpha barrel]]
	[[Category: Anti-parallel beta-sheet]]		[[Category: Anti-parallel beta-sheet]]
-		+	[[Category: Lyase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 18:32:01 2009''~~	+

OCA at 16:32, 17 February 2009

2009-02-17T16:32:02Z

←Older revision		Revision as of 16:32, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1J0M is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA].	+	1J0M is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0M OCA].

	==Reference==		==Reference==
-	~~Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan., Hashimoto W, Nankai H, Mikami B, Murata K, J Biol Chem. 2003 Feb 28;278(9):7663-73. Epub 2002 Dec 9.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12475987 12475987]~~	+	<ref group="xtra">PMID:12475987</ref><references group="xtra"/>
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
-	[[Category: Single protein]]
	[[Category: Xanthan lyase]]		[[Category: Xanthan lyase]]
	[[Category: Hashimoto, W.]]		[[Category: Hashimoto, W.]]
Line 34:		Line 33:
	[[Category: Anti-parallel beta-sheet]]		[[Category: Anti-parallel beta-sheet]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 1 14~~:19:~~03 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:32:01 2009''

OCA at 11:19, 1 July 2008

2008-07-01T11:19:05Z

←Older revision		Revision as of 11:19, 1 July 2008
Line 1:		Line 1:
-	[[Image:1j0m.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1j0m.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1j0m\| PDB=1j0m \| SCENE= }}		{{STRUCTURE_1j0m\| PDB=1j0m \| SCENE= }}

-	~~'''~~Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan~~'''~~	+	===Crystal Structure of Bacillus sp. GL1 Xanthan Lyase that Acts on Side Chains of Xanthan===


-	~~==Overview==~~	+	<!--
-	~~Xanthan lyase~~, ~~a member of polysaccharide lyase family 8~~, ~~is a key enzyme for complete depolymerization of a bacterial heteropolysaccharide, xanthan, in Bacillus sp. GL1. The enzyme acts exolytically on~~ the ~~side chains of~~ the polysaccharide. The x-ray crystallographic structure of xanthan lyase was determined by the multiple isomorphous replacement method. The crystal structures of xanthan lyase and its complex with the product (~~pyruvylated mannose) were refined~~ at 2.~~3 and 2~~.4 A resolution with final R-factors of 17.5 and 16.9%, respectively. The refined structure of the product-free enzyme comprises 752 amino acid residues, 248 water molecules, and one calcium ion. The enzyme consists of N-terminal alpha-helical and C-terminal beta-sheet domains, which constitute incomplete alpha(5)~~/alpha(5)-barrel and anti-parallel beta-sheet structures~~, ~~respectively. A deep cleft~~ is ~~located in~~ the ~~N-terminal alpha-helical domain facing the interface between the two domains~~. Although the overall structure of the enzyme is basically the same as that of the family 8 lyases for hyaluronate and chondroitin AC, significant differences were observed in the loop structure over the cleft. The crystal structure of the xanthan lyase complexed with pyruvylated mannose indicates that the sugar-~~binding site is located in the deep cleft, where aromatic and positively charged amino acid residues are involved in the binding. The Arg(313) and Tyr(315) residues in the loop from the N~~-terminal domain and the Arg(612) residue in the loop from the C-terminal domain directly bind to the pyruvate moiety of the product through the formation of hydrogen bonds, thus determining the substrate specificity of the enzyme.	+	The line below this paragraph, {{ABSTRACT_PUBMED_12475987}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 12475987 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_12475987}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: Alpha/alpha barrel]]		[[Category: Alpha/alpha barrel]]
	[[Category: Anti-parallel beta-sheet]]		[[Category: Anti-parallel beta-sheet]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May~~ ~~2 20~~:39:30 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 14:19:03 2008''