1rwa - Revision history

OCA at 08:26, 14 February 2024

OCA — Wed, 14 Feb 2024 08:26:19 GMT

←Older revision		Revision as of 08:26, 14 February 2024
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	<StructureSection load='1rwa' size='340' side='right'caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1rwa' size='340' side='right'caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arthrobacter_aurescens Arthrobacter~~ aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RWA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenarthrobacter_aurescens Paenarthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RWA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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]] 1.3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5]~~ </~~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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [https://pdbe.org/1rwa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [https://www.ebi.ac.uk/pdbsum/1rwa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwa 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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [https://pdbe.org/1rwa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [https://www.ebi.ac.uk/pdbsum/1rwa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/P84141_PAEAU P84141_PAEAU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=1rwa 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=1rwa ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of cleaving hyaluronan. We have determined the three-dimensional crystal structure of ArthroAC in its native form as well as in complex with its substrates (chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence of ArthroAC has not been previously determined but it was possible to determine the amino acid sequence of this enzyme from the high-resolution electron density maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were obtained by soaking the substrate into the crystals for varying lengths of time (30 seconds to ten hours) and flash-cooling the crystals. The electron density map for crystals soaked in the substrate for as short as 30 seconds showed the substrate clearly and indicated that the ring of central glucuronic acid assumes a distorted boat conformation. This structure strongly supports the lytic mechanism where Tyr242 acts as a general base that abstracts the proton from the C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on the glucuronate acidic group. Comparison of this structure with that of chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an explanation for the exolytic and endolytic mode of action of ArthroAC and FlavoAC, respectively.
-
-	High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism.,Lunin VV, Li Y, Linhardt RJ, Miyazono H, Kyogashima M, Kaneko T, Bell AW, Cygler M J Mol Biol. 2004 Mar 19;337(2):367-86. PMID:15003453<ref>PMID:15003453</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1rwa" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arthrobacter aurescens]]
-	[[Category: Chondroitin AC lyase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bell~~, A W~~]]	+	[[Category: Paenarthrobacter aurescens]]
-	[[Category: Cygler, M]]	+	[[Category: Bell AW]]
-	[[Category: Kyogashima, M]]	+	[[Category: Cygler M]]
-	[[Category: Li, Y]]	+	[[Category: Kyogashima M]]
-	[[Category: Lunin~~, V V~~]]	+	[[Category: Li Y]]
-	[[Category: Miyazono, H]]	+	[[Category: Lunin VV]]
-	~~[[Category: Chondroitin lyase]]~~	+	[[Category: Miyazono H]]
-	~~[[Category: Chondroitinase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 07:23, 22 September 2021

OCA — Wed, 22 Sep 2021 07:23:15 GMT

←Older revision		Revision as of 07:23, 22 September 2021
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	<StructureSection load='1rwa' size='340' side='right'caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1rwa' size='340' side='right'caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RWA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RWA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [~~http~~://pdbe.org/1rwa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rwa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwa 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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [https://pdbe.org/1rwa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [https://www.ebi.ac.uk/pdbsum/1rwa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwa ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 19:48, 11 December 2019

OCA — Wed, 11 Dec 2019 19:48:44 GMT

←Older revision		Revision as of 19:48, 11 December 2019
Line 1:		Line 1:

	==Crystal structure of Arthrobacter aurescens chondroitin AC lyase==		==Crystal structure of Arthrobacter aurescens chondroitin AC lyase==
-	<StructureSection load='1rwa' size='340' side='right' caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='1rwa' size='340' side='right'caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RWA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RWA FirstGlance]. <br>
Line 34:		Line 34:
	[[Category: Arthrobacter aurescens]]		[[Category: Arthrobacter aurescens]]
	[[Category: Chondroitin AC lyase]]		[[Category: Chondroitin AC lyase]]
		+	[[Category: Large Structures]]
	[[Category: Bell, A W]]		[[Category: Bell, A W]]
	[[Category: Cygler, M]]		[[Category: Cygler, M]]

OCA at 07:19, 8 March 2018

OCA — Thu, 08 Mar 2018 07:19:07 GMT

←Older revision		Revision as of 07:19, 8 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of Arthrobacter aurescens chondroitin AC lyase==		==Crystal structure of Arthrobacter aurescens chondroitin AC lyase==
	<StructureSection load='1rwa' size='340' side='right' caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1rwa' size='340' side='right' caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [http://pdbe.org/1rwa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [http://www.ebi.ac.uk/pdbsum/1rwa 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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [http://pdbe.org/1rwa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [http://www.ebi.ac.uk/pdbsum/1rwa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwa 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/rw/1rwa_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rw/1rwa_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 16:05, 9 February 2016

OCA — Tue, 09 Feb 2016 16:05:50 GMT

←Older revision		Revision as of 16:05, 9 February 2016
Line 16:		Line 16:
	<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=1rwa ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:51, 10 September 2015

OCA — Thu, 10 Sep 2015 23:51:06 GMT

←Older revision		Revision as of 23:51, 10 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [http://www.ebi.ac.uk/pdbsum/1rwa 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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [http://pdbe.org/1rwa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [http://www.ebi.ac.uk/pdbsum/1rwa 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 1rwa" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:32, 6 January 2015

OCA — Tue, 06 Jan 2015 08:32:09 GMT

←Older revision		Revision as of 08:32, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RWA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RWA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [http://www.ebi.ac.uk/pdbsum/1rwa 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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [http://www.ebi.ac.uk/pdbsum/1rwa 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 32:		Line 32:
	[[Category: Arthrobacter aurescens]]		[[Category: Arthrobacter aurescens]]
	[[Category: Chondroitin AC lyase]]		[[Category: Chondroitin AC lyase]]
-	[[Category: Bell, A W.]]	+	[[Category: Bell, A W]]
-	[[Category: Cygler, M.]]	+	[[Category: Cygler, M]]
-	[[Category: Kyogashima, M.]]	+	[[Category: Kyogashima, M]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
-	[[Category: Lunin, V V.]]	+	[[Category: Lunin, V V]]
-	[[Category: Miyazono, H.]]	+	[[Category: Miyazono, H]]
	[[Category: Chondroitin lyase]]		[[Category: Chondroitin lyase]]
	[[Category: Chondroitinase]]		[[Category: Chondroitinase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 09:10, 3 October 2014

OCA — Fri, 03 Oct 2014 09:10:30 GMT

←Older revision		Revision as of 09:10, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1rwa\| PDB~~=1rwa \| ~~SCENE~~= }}	+	==Crystal structure of Arthrobacter aurescens chondroitin AC lyase==
-	===~~Crystal~~ structure of Arthrobacter aurescens ~~chondroitin~~ AC lyase===	+	<StructureSection load='1rwa' size='340' side='right' caption='[[1rwa]], [[Resolution\|resolution]] 1.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_15003453}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rwa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RWA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rw9\|1rw9]], [[1rwc\|1rwc]], [[1rwf\|1rwf]], [[1rwg\|1rwg]], [[1rwh\|1rwh]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </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=1rwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rwa RCSB], [http://www.ebi.ac.uk/pdbsum/1rwa 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/rw/1rwa_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 ==
		+	Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of cleaving hyaluronan. We have determined the three-dimensional crystal structure of ArthroAC in its native form as well as in complex with its substrates (chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence of ArthroAC has not been previously determined but it was possible to determine the amino acid sequence of this enzyme from the high-resolution electron density maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were obtained by soaking the substrate into the crystals for varying lengths of time (30 seconds to ten hours) and flash-cooling the crystals. The electron density map for crystals soaked in the substrate for as short as 30 seconds showed the substrate clearly and indicated that the ring of central glucuronic acid assumes a distorted boat conformation. This structure strongly supports the lytic mechanism where Tyr242 acts as a general base that abstracts the proton from the C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on the glucuronate acidic group. Comparison of this structure with that of chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an explanation for the exolytic and endolytic mode of action of ArthroAC and FlavoAC, respectively.

-	~~==About this Structure==~~	+	High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism.,Lunin VV, Li Y, Linhardt RJ, Miyazono H, Kyogashima M, Kaneko T, Bell AW, Cygler M J Mol Biol. 2004 Mar 19;337(2):367-86. PMID:15003453<ref>PMID:15003453</ref>
-	~~[[1rwa]] is a 1 chain~~ structure ~~with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_aurescens~~ Arthrobacter aurescens~~]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1RWA OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:015003453</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Arthrobacter aurescens]]		[[Category: Arthrobacter aurescens]]
	[[Category: Chondroitin AC lyase]]		[[Category: Chondroitin AC lyase]]

OCA at 11:05, 16 April 2014

OCA — Wed, 16 Apr 2014 11:05:16 GMT

←Older revision		Revision as of 11:05, 16 April 2014
Line 1:		Line 1:
-	[[Image:1rwa.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1rwa", 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_1rwa\| PDB=1rwa \| SCENE= }}		{{STRUCTURE_1rwa\| PDB=1rwa \| SCENE= }}
-
	===Crystal structure of Arthrobacter aurescens chondroitin AC lyase===		===Crystal structure of Arthrobacter aurescens chondroitin AC lyase===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15003453}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15003453 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15003453}}		{{ABSTRACT_PUBMED_15003453}}

Line 22:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:015003453</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015003453</ref><references group="xtra"/><references/>
	[[Category: Arthrobacter aurescens]]		[[Category: Arthrobacter aurescens]]
	[[Category: Chondroitin AC lyase]]		[[Category: Chondroitin AC lyase]]

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

OCA — Wed, 09 May 2012 08:28:03 GMT

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

←Older revision

Revision as of 08:28, 9 May 2012