3wiw - Revision history

OCA at 13:12, 8 November 2023

OCA — Wed, 08 Nov 2023 13:12:39 GMT

←Older revision		Revision as of 13:12, 8 November 2023
Line 1:		Line 1:

	==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==		==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==
-	<StructureSection load='3wiw' size='340' side='right'caption='[[3wiw]]' scene=''>	+	<StructureSection load='3wiw' size='340' side='right'caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wiw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pedobacter_heparinus_DSM_2366 Pedobacter heparinus DSM 2366]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIW FirstGlance]. <br>
-	</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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [https://pdbe.org/3wiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [https://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw ProSAT]</span></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]] 1.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [https://pdbe.org/3wiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [https://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/C6Y1N7_PEDHD C6Y1N7_PEDHD]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Extracellular matrix molecules such as glycosaminoglycans (GAGs) are typical targets for some pathogenic bacteria, which allow adherence to host cells. Bacterial polysaccharide lyases depolymerize GAGs in beta-elimination reactions, and the resulting unsaturated disaccharides are subsequently degraded to constituent monosaccharides by unsaturated glucuronyl hydrolases (UGLs). UGL substrates are classified as 1,3- and 1,4-types based on the glycoside bonds. Unsaturated chondroitin and heparin disaccharides are typical members of 1,3- and 1,4-types, respectively. Here we show the reaction modes of bacterial UGLs with unsaturated heparin disaccharides by X-ray crystallography, docking simulation, and site-directed mutagenesis. Although streptococcal and bacillus UGLs were active on unsaturated heparin disaccharides, those preferred 1,3- rather than 1,4-type substrates. The genome of GAG-degrading Pedobacter heparinus encodes 13 UGLs. Of these, Phep_2830 is known to be specific for unsaturated heparin disaccharides. The crystal structure of Phep_2830 was determined at 1.35 A resolution. In comparison with structures of streptococcal and bacillus UGLs, a pocket-like structure and lid loop at subsite +1 are characteristic of Phep_2830. Docking simulations of Phep_2830 with unsaturated heparin disaccharides demonstrated that the direction of substrate pyranose rings differs from that in unsaturated chondroitin disaccharides. Acetyl groups of unsaturated heparin disaccharides are well accommodated in the pocket at subsite +1, and aromatic residues of the lid loop are required for stacking interactions with substrates. Thus, site-directed mutations of the pocket and lid loop led to significantly reduced enzyme activity, suggesting that the pocket-like structure and lid loop are involved in the recognition of 1,4-type substrates by UGLs.
		+
		+	Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin.,Nakamichi Y, Mikami B, Murata K, Hashimoto W J Biol Chem. 2014 Jan 8. PMID:24403065<ref>PMID:24403065</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3wiw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pedobacter heparinus DSM 2366]]
	[[Category: Hashimoto W]]		[[Category: Hashimoto W]]
	[[Category: Mikami B]]		[[Category: Mikami B]]
	[[Category: Murata K]]		[[Category: Murata K]]
	[[Category: Nakamichi Y]]		[[Category: Nakamichi Y]]

OCA at 10:32, 31 August 2022

OCA — Wed, 31 Aug 2022 10:32:40 GMT

←Older revision		Revision as of 10:32, 31 August 2022
Line 1:		Line 1:

	==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==		==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==
-	<StructureSection load='3wiw' size='340' side='right'caption='[[3wiw]]~~, [[Resolution\|resolution]] 1.35Å~~' scene=''>	+	<StructureSection load='3wiw' size='340' side='right'caption='[[3wiw]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3wiw]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>	+	</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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [https://pdbe.org/3wiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [https://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zzr\|2zzr]], [[2fv1\|2fv1]]</div></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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [https://pdbe.org/3wiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [https://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Extracellular matrix molecules such as glycosaminoglycans (GAGs) are typical targets for some pathogenic bacteria, which allow adherence to host cells. Bacterial polysaccharide lyases depolymerize GAGs in beta-elimination reactions, and the resulting unsaturated disaccharides are subsequently degraded to constituent monosaccharides by unsaturated glucuronyl hydrolases (UGLs). UGL substrates are classified as 1,3- and 1,4-types based on the glycoside bonds. Unsaturated chondroitin and heparin disaccharides are typical members of 1,3- and 1,4-types, respectively. Here we show the reaction modes of bacterial UGLs with unsaturated heparin disaccharides by X-ray crystallography, docking simulation, and site-directed mutagenesis. Although streptococcal and bacillus UGLs were active on unsaturated heparin disaccharides, those preferred 1,3- rather than 1,4-type substrates. The genome of GAG-degrading Pedobacter heparinus encodes 13 UGLs. Of these, Phep_2830 is known to be specific for unsaturated heparin disaccharides. The crystal structure of Phep_2830 was determined at 1.35 A resolution. In comparison with structures of streptococcal and bacillus UGLs, a pocket-like structure and lid loop at subsite +1 are characteristic of Phep_2830. Docking simulations of Phep_2830 with unsaturated heparin disaccharides demonstrated that the direction of substrate pyranose rings differs from that in unsaturated chondroitin disaccharides. Acetyl groups of unsaturated heparin disaccharides are well accommodated in the pocket at subsite +1, and aromatic residues of the lid loop are required for stacking interactions with substrates. Thus, site-directed mutations of the pocket and lid loop led to significantly reduced enzyme activity, suggesting that the pocket-like structure and lid loop are involved in the recognition of 1,4-type substrates by UGLs.
-
-	Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin.,Nakamichi Y, Mikami B, Murata K, Hashimoto W J Biol Chem. 2014 Jan 8. PMID:24403065<ref>PMID:24403065</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3wiw" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hashimoto, W]]	+	[[Category: Hashimoto W]]
-	[[Category: Mikami, B]]	+	[[Category: Mikami B]]
-	[[Category: Murata, K]]	+	[[Category: Murata K]]
-	[[Category: Nakamichi, Y]]	+	[[Category: Nakamichi Y]]
-	~~[[Category: Alpha6/alpha6-barrel]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 04:57, 25 August 2022

OCA — Thu, 25 Aug 2022 04:57:57 GMT

←Older revision		Revision as of 04:57, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='3wiw' size='340' side='right'caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='3wiw' size='340' side='right'caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wiw]] is a 1 chain structure ~~with sequence from [https://en.wikipedia.org/wiki/Pedhd Pedhd]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wiw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zzr\|2zzr]], [[2fv1\|2fv1]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zzr\|2zzr]], [[2fv1\|2fv1]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Phep_2830 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485917 PEDHD])</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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [https://pdbe.org/3wiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [https://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw 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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [https://pdbe.org/3wiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [https://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pedhd]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]
	[[Category: Mikami, B]]		[[Category: Mikami, B]]

OCA at 05:38, 3 August 2022

OCA — Wed, 03 Aug 2022 05:38:17 GMT

←Older revision		Revision as of 05:38, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==		==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==
-	<StructureSection load='3wiw' size='340' side='right' caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>	+	<StructureSection load='3wiw' size='340' side='right'caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wiw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pedhd Pedhd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wiw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pedhd Pedhd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zzr\|2zzr]], [[2fv1\|2fv1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zzr\|2zzr]], [[2fv1\|2fv1]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Phep_2830 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485917 PEDHD])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Phep_2830 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485917 PEDHD])</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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [~~http~~://pdbe.org/3wiw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw 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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [https://pdbe.org/3wiw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [https://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pedhd]]		[[Category: Pedhd]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]

OCA at 18:16, 4 August 2016

OCA — Thu, 04 Aug 2016 18:16:53 GMT

←Older revision		Revision as of 18:16, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==		==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==
	<StructureSection load='3wiw' size='340' side='right' caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='3wiw' size='340' side='right' caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zzr\|2zzr]], [[2fv1\|2fv1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zzr\|2zzr]], [[2fv1\|2fv1]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Phep_2830 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485917 PEDHD])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Phep_2830 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485917 PEDHD])</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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [http://www.ebi.ac.uk/pdbsum/3wiw 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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [http://pdbe.org/3wiw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [http://www.ebi.ac.uk/pdbsum/3wiw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wiw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3wiw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:10, 21 December 2014

OCA — Sun, 21 Dec 2014 18:10:21 GMT

←Older revision		Revision as of 18:10, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3wiw\| PDB=3wiw \| SCENE= }}~~	+	==Crystal structure of unsaturated glucuronyl hydrolase specific for heparin==
-	===Crystal structure of unsaturated glucuronyl hydrolase specific for heparin===	+	<StructureSection load='3wiw' size='340' side='right' caption='[[3wiw]], [[Resolution\|resolution]] 1.35Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24403065}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wiw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pedhd Pedhd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WIW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zzr\|2zzr]], [[2fv1\|2fv1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Phep_2830 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485917 PEDHD])</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=3wiw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wiw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wiw RCSB], [http://www.ebi.ac.uk/pdbsum/3wiw PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Extracellular matrix molecules such as glycosaminoglycans (GAGs) are typical targets for some pathogenic bacteria, which allow adherence to host cells. Bacterial polysaccharide lyases depolymerize GAGs in beta-elimination reactions, and the resulting unsaturated disaccharides are subsequently degraded to constituent monosaccharides by unsaturated glucuronyl hydrolases (UGLs). UGL substrates are classified as 1,3- and 1,4-types based on the glycoside bonds. Unsaturated chondroitin and heparin disaccharides are typical members of 1,3- and 1,4-types, respectively. Here we show the reaction modes of bacterial UGLs with unsaturated heparin disaccharides by X-ray crystallography, docking simulation, and site-directed mutagenesis. Although streptococcal and bacillus UGLs were active on unsaturated heparin disaccharides, those preferred 1,3- rather than 1,4-type substrates. The genome of GAG-degrading Pedobacter heparinus encodes 13 UGLs. Of these, Phep_2830 is known to be specific for unsaturated heparin disaccharides. The crystal structure of Phep_2830 was determined at 1.35 A resolution. In comparison with structures of streptococcal and bacillus UGLs, a pocket-like structure and lid loop at subsite +1 are characteristic of Phep_2830. Docking simulations of Phep_2830 with unsaturated heparin disaccharides demonstrated that the direction of substrate pyranose rings differs from that in unsaturated chondroitin disaccharides. Acetyl groups of unsaturated heparin disaccharides are well accommodated in the pocket at subsite +1, and aromatic residues of the lid loop are required for stacking interactions with substrates. Thus, site-directed mutations of the pocket and lid loop led to significantly reduced enzyme activity, suggesting that the pocket-like structure and lid loop are involved in the recognition of 1,4-type substrates by UGLs.

-	~~==About this Structure==~~	+	Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin.,Nakamichi Y, Mikami B, Murata K, Hashimoto W J Biol Chem. 2014 Jan 8. PMID:24403065<ref>PMID:24403065</ref>
-	~~[[3wiw]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3WIW OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024403065</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Hashimoto, W.]]	+	== References ==
-	[[Category: Mikami, B.]]	+	<references/>
-	[[Category: Murata, K.]]	+	__TOC__
-	[[Category: Nakamichi, Y.]]	+	</StructureSection>
		+	[[Category: Pedhd]]
		+	[[Category: Hashimoto, W]]
		+	[[Category: Mikami, B]]
		+	[[Category: Murata, K]]
		+	[[Category: Nakamichi, Y]]
	[[Category: Alpha6/alpha6-barrel]]		[[Category: Alpha6/alpha6-barrel]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 04:24, 13 February 2014

OCA — Thu, 13 Feb 2014 04:24:37 GMT

←Older revision		Revision as of 04:24, 13 February 2014
Line 1:		Line 1:
	{{STRUCTURE_3wiw\| PDB=3wiw \| SCENE= }}		{{STRUCTURE_3wiw\| PDB=3wiw \| SCENE= }}
	===Crystal structure of unsaturated glucuronyl hydrolase specific for heparin===		===Crystal structure of unsaturated glucuronyl hydrolase specific for heparin===
		+	{{ABSTRACT_PUBMED_24403065}}

	==About this Structure==		==About this Structure==
	[[3wiw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA].		[[3wiw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024403065</ref><references group="xtra"/><references/>
	[[Category: Hashimoto, W.]]		[[Category: Hashimoto, W.]]
	[[Category: Mikami, B.]]		[[Category: Mikami, B.]]

OCA at 10:34, 8 January 2014

OCA — Wed, 08 Jan 2014 10:34:53 GMT

←Older revision		Revision as of 10:34, 8 January 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3wiw\| PDB=3wiw \| SCENE= }}
		+	===Crystal structure of unsaturated glucuronyl hydrolase specific for heparin===

-	~~The entry~~ 3wiw is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3wiw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIW OCA].
-	~~Authors~~: ~~Nakamichi~~, Y., Mikami, B., Murata, K., ~~Hashimoto, W~~.	+	[[Category: Hashimoto, W.]]
-		+	[[Category: Mikami, B.]]
-	~~Description~~: ~~Crystal structure of unsaturated glucuronyl hydrolase specific for heparin~~	+	[[Category: Murata, K.]]
		+	[[Category: Nakamichi, Y.]]
		+	[[Category: Alpha6/alpha6-barrel]]
		+	[[Category: Hydrolase]]

OCA at 05:24, 10 October 2013

OCA — Thu, 10 Oct 2013 05:24:04 GMT

←Older revision		Revision as of 05:24, 10 October 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3wiw is ON HOLD	+	The entry 3wiw is ON HOLD until Paper Publication

	Authors: Nakamichi, Y., Mikami, B., Murata, K., Hashimoto, W.		Authors: Nakamichi, Y., Mikami, B., Murata, K., Hashimoto, W.

	Description: Crystal structure of unsaturated glucuronyl hydrolase specific for heparin		Description: Crystal structure of unsaturated glucuronyl hydrolase specific for heparin

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

OCA — Wed, 02 Oct 2013 06:29:18 GMT

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

←Older revision

Revision as of 06:29, 2 October 2013