3e7j - Revision history

OCA at 12:59, 30 August 2023

OCA — Wed, 30 Aug 2023 12:59:20 GMT

←Older revision		Revision as of 12:59, 30 August 2023
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	<StructureSection load='3e7j' size='340' side='right'caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3e7j' size='340' side='right'caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_13125 Atcc 13125~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E7J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~"><~~scene name~~='~~pdbligand~~=~~ACT~~:~~ACETATE+ION'~~>~~ACT~~</~~scene~~>, <scene name='pdbligand=ZN:~~ZINC~~+ION'>ZN</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.1Å</td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[3e80\|3e80]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [https://pdbe.org/3e7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [https://www.ebi.ac.uk/pdbsum/3e7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7j 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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [https://pdbe.org/3e7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [https://www.ebi.ac.uk/pdbsum/3e7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HEPB_PEDHD HEPB_PEDHD]] Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.<ref>PMID:8702264</ref>	+	[https://www.uniprot.org/uniprot/HEPB_PEDHD HEPB_PEDHD] Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.<ref>PMID:8702264</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 13125]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cygler, M~~]]	+	[[Category: Pedobacter heparinus]]
-	[[Category: ~~Shaya, D~~]]	+	[[Category: Cygler M]]
-	[[Category: ~~Alpha and beta lyase]]~~	+	[[Category: Shaya D]]
-	~~[[Category: Alpha6/alpha6 incomplete toroid]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 19:36, 20 October 2021

OCA — Wed, 20 Oct 2021 19:36:42 GMT

←Older revision		Revision as of 19:36, 20 October 2021
Line 3:		Line 3:
	<StructureSection load='3e7j' size='340' side='right'caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3e7j' size='340' side='right'caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_13125 Atcc 13125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3E7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_13125 Atcc 13125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG~~</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e80\|3e80]]</div></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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [~~http~~://pdbe.org/3e7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3e7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7j 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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [https://pdbe.org/3e7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [https://www.ebi.ac.uk/pdbsum/3e7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/HEPB_PEDHD HEPB_PEDHD]] Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.<ref>PMID:8702264</ref>	+	[[https://www.uniprot.org/uniprot/HEPB_PEDHD HEPB_PEDHD]] Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.<ref>PMID:8702264</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:01, 3 June 2020

OCA — Wed, 03 Jun 2020 07:01:09 GMT

←Older revision		Revision as of 07:01, 3 June 2020
Line 1:		Line 1:

	==HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate==		==HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate==
-	<StructureSection load='3e7j' size='340' side='right' caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3e7j' size='340' side='right'caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_13125 Atcc 13125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3E7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_13125 Atcc 13125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3E7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://pdbe.org/3e7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7j 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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://pdbe.org/3e7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 13125]]		[[Category: Atcc 13125]]
		+	[[Category: Large Structures]]
	[[Category: Cygler, M]]		[[Category: Cygler, M]]
	[[Category: Shaya, D]]		[[Category: Shaya, D]]

OCA at 07:42, 29 August 2018

OCA — Wed, 29 Aug 2018 07:42:57 GMT

←Older revision		Revision as of 07:42, 29 August 2018
Line 3:		Line 3:
	<StructureSection load='3e7j' size='340' side='right' caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3e7j' size='340' side='right' caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pedobacter_heparinus Pedobacter heparinus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_13125 Atcc 13125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E7J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</td></tr>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e7/3e7j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e7/3e7j_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pedobacter heparinus~~]]	+	[[Category: Atcc 13125]]
	[[Category: Cygler, M]]		[[Category: Cygler, M]]
	[[Category: Shaya, D]]		[[Category: Shaya, D]]

OCA at 09:04, 25 October 2017

OCA — Wed, 25 Oct 2017 09:04:30 GMT

←Older revision		Revision as of 09:04, 25 October 2017
Line 1:		Line 1:
		+
	==HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate==		==HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate==
	<StructureSection load='3e7j' size='340' side='right' caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3e7j' size='340' side='right' caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT~~</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN~~</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://pdbe.org/3e7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j 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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://pdbe.org/3e7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 03:37, 10 February 2016

OCA — Wed, 10 Feb 2016 03:37:14 GMT

←Older revision		Revision as of 03:37, 10 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j 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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://pdbe.org/3e7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Q46080_PEDHE Q46080_PEDHE~~]] Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.<ref>PMID:8702264</ref>	+	[[http://www.uniprot.org/uniprot/HEPB_PEDHD HEPB_PEDHD]] Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.<ref>PMID:8702264</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=3e7j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3e7j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:31, 25 December 2014

OCA — Thu, 25 Dec 2014 11:31:24 GMT

←Older revision		Revision as of 11:31, 25 December 2014
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	<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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j 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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q46080_PEDHE Q46080_PEDHE]] Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.<ref>PMID:8702264</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:27, 19 November 2014

OCA — Wed, 19 Nov 2014 13:27:48 GMT

←Older revision		Revision as of 13:27, 19 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3e7j.~~png~~\|~~left~~\|200px]]	+	==HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate==
		+	<StructureSection load='3e7j' size='340' side='right' caption='[[3e7j]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E7J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e80\|3e80]]</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=3e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e7j RCSB], [http://www.ebi.ac.uk/pdbsum/3e7j 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/e7/3e7j_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 ==
		+	Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Recently, we determined the crystal structure of HepII from Pedobacter heparinus (previously known as Flavobacterium heparinum) in complex with a heparin disaccharide product, and identified the location of its active site. Here we present the structure of HepII complexed with a heparan sulfate disaccharide product, proving that the same binding/active site is responsible for the degradation of both uronic acid epimers containing substrates. The key enzymatic step involves removal of a proton from the C5 carbon (a chiral center) of the uronic acid, posing a topological challenge to abstract the proton from either side of the ring in a single active site. We have identified three potential active site residues equidistant from C5 and located on both sides of the uronate product and determined their role in catalysis using a set of defined tetrasaccharide substrates. HepII H202A/Y257A mutant lost activity for both substrates and we determined its crystal structure complexed with a heparan sulfate-derived tetrasaccharide. Based on kinetic characterization of various mutants and the structure of the enzyme-substrate complex we propose residues participating in catalysis and their specific roles.

-	~~{{STRUCTURE_3e7j\| PDB=3e7j \| SCENE= }}~~	+	Catalytic mechanism of heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate.,Shaya D, Zhao W, Garron ML, Xiao Z, Cui Q, Zhang Z, Sulea T, Linhardt RJ, Cygler M J Biol Chem. 2010 Jun 25;285(26):20051-61. Epub 2010 Apr 19. PMID:20404324<ref>PMID:20404324</ref>

-	~~===HeparinaseII H202A~~/~~Y257A double mutant complexed with~~ a ~~heparan sulfate tetrasaccharide substrate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20404324}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3e7j]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pedobacter_heparinus Pedobacter heparinus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:020404324<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pedobacter heparinus]]		[[Category: Pedobacter heparinus]]
-	[[Category: Cygler, M.]]	+	[[Category: Cygler, M]]
-	[[Category: Shaya, D.]]	+	[[Category: Shaya, D]]
	[[Category: Alpha and beta lyase]]		[[Category: Alpha and beta lyase]]
	[[Category: Alpha6/alpha6 incomplete toroid]]		[[Category: Alpha6/alpha6 incomplete toroid]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA: Protected "3e7j" [edit=sysop:move=sysop]

OCA — Wed, 09 Jan 2013 08:54:26 GMT

Protected "3e7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:54, 9 January 2013

OCA at 08:54, 9 January 2013

OCA — Wed, 09 Jan 2013 08:54:22 GMT

←Older revision		Revision as of 08:54, 9 January 2013
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-	{{Seed}}
	[[Image:3e7j.png\|left\|200px]]		[[Image:3e7j.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3e7j", 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_3e7j\| PDB=3e7j \| SCENE= }}		{{STRUCTURE_3e7j\| PDB=3e7j \| SCENE= }}

	===HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate===		===HeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20404324}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20404324 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20404324}}		{{ABSTRACT_PUBMED_20404324}}

	==About this Structure==		==About this Structure==
-	~~3E7J~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA].	+	[[3e7j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7J OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20404324~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020404324</ref><references group="xtra"/>
	[[Category: Pedobacter heparinus]]		[[Category: Pedobacter heparinus]]
	[[Category: Cygler, M.]]		[[Category: Cygler, M.]]
Line 31:		Line 19:
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 1 09:14:32 2010''