2eac - Revision history

OCA at 00:53, 21 November 2024

2024-11-21T00:53:16Z

← Older revision		Revision as of 00:53, 21 November 2024
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	<StructureSection load='2eac' size='340' side='right'caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2eac' size='340' side='right'caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"actinobacterium_bifidum"_(tissier_1900)_puntoni_1937 "actinobacterium~~ bifidum~~" (tissier 1900) puntoni 1937~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EAC 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>~~, ~~<scene name='pdbligand=DFU:(2S,3R,4S,5R)-~~2~~-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</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;~~'>~~[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]~~</~~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>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1~~,2-~~alpha~~-~~L-fucosidase 1~~,~~2-alpha-L-fucosidase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63]~~ </~~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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [https://pdbe.org/2eac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [https://www.ebi.ac.uk/pdbsum/2eac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eac 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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [https://pdbe.org/2eac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [https://www.ebi.ac.uk/pdbsum/2eac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eac ProSAT]</span></td></tr>
	</table>		</table>
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ea/2eac_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ea/2eac_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~1,2-alpha-L-fucosidase~~]]		[[Category: Bifidobacterium bifidum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Katayama, T]]		[[Category: Katayama T]]
	[[Category: Kato, R]]		[[Category: Kato R]]
	[[Category: Nagae, M]]		[[Category: Nagae M]]
	[[Category: Tsuchiya, A]]		[[Category: Tsuchiya A]]
	[[Category: Wakatsuki, S]]		[[Category: Wakatsuki S]]
	[[Category: Yamamoto, K]]		[[Category: Yamamoto K]]
	~~[[Category: Fucosidase]]~~
	~~[[Category: Glycoside hydrolase]]~~
	~~[[Category: Hydrolase~~]]

OCA at 17:22, 15 December 2021

2021-12-15T17:22:41Z

← Older revision		Revision as of 17:22, 15 December 2021
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	<StructureSection load='2eac' size='340' side='right'caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2eac' size='340' side='right'caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"actinobacterium_bifidum"_(tissier_1900)_puntoni_1937 "actinobacterium bifidum" (tissier 1900) puntoni 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2EAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinobacterium_bifidum"_(tissier_1900)_puntoni_1937 "actinobacterium bifidum" (tissier 1900) puntoni 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EAC 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>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</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>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [~~http~~://pdbe.org/2eac PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2eac PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2eac 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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [https://pdbe.org/2eac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [https://www.ebi.ac.uk/pdbsum/2eac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eac ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:30, 11 March 2020

2020-03-11T08:30:29Z

← Older revision		Revision as of 08:30, 11 March 2020
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	==Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin==		==Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin==
	<StructureSection load='2eac' size='340' side='right' caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2eac' size='340' side='right'caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinobacterium_bifidum"_(tissier_1900)_puntoni_1937 "actinobacterium bifidum" (tissier 1900) puntoni 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinobacterium_bifidum"_(tissier_1900)_puntoni_1937 "actinobacterium bifidum" (tissier 1900) puntoni 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAC FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: 1,2-alpha-L-fucosidase]]		[[Category: 1,2-alpha-L-fucosidase]]
			[[Category: Large Structures]]
	[[Category: Katayama, T]]		[[Category: Katayama, T]]
	[[Category: Kato, R]]		[[Category: Kato, R]]

OCA at 07:11, 6 June 2018

2018-06-06T07:11:19Z

← Older revision		Revision as of 07:11, 6 June 2018
Line 1:		Line 1:

	==Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin==		==Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin==
	<StructureSection load='2eac' size='340' side='right' caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2eac' size='340' side='right' caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [http://pdbe.org/2eac PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [http://www.ebi.ac.uk/pdbsum/2eac 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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [http://pdbe.org/2eac PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [http://www.ebi.ac.uk/pdbsum/2eac PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2eac 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/ea/2eac_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ea/2eac_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>
	</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=2eac ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:51, 11 September 2015

2015-09-11T14:51:30Z

← Older revision		Revision as of 14:51, 11 September 2015
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	<StructureSection load='2eac' size='340' side='right' caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2eac' size='340' side='right' caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bifidobacterium_bifidum Bifidobacterium~~ bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinobacterium_bifidum"_(tissier_1900)_puntoni_1937 "actinobacterium bifidum" (tissier 1900) puntoni 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAC 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>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</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>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [http://www.ebi.ac.uk/pdbsum/2eac 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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [http://pdbe.org/2eac PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [http://www.ebi.ac.uk/pdbsum/2eac 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 2eac" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: 1,2-alpha-L-fucosidase]]		[[Category: 1,2-alpha-L-fucosidase]]
	~~[[Category: Bifidobacterium bifidum]]~~
	[[Category: Katayama, T]]		[[Category: Katayama, T]]
	[[Category: Kato, R]]		[[Category: Kato, R]]

OCA at 18:31, 15 January 2015

2015-01-15T18:31:08Z

← Older revision		Revision as of 18:31, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAC FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</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>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [http://www.ebi.ac.uk/pdbsum/2eac 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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [http://www.ebi.ac.uk/pdbsum/2eac 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: 1,2-alpha-L-fucosidase]]		[[Category: 1,2-alpha-L-fucosidase]]
	[[Category: Bifidobacterium bifidum]]		[[Category: Bifidobacterium bifidum]]
	[[Category: Katayama, T.]]		[[Category: Katayama, T]]
	[[Category: Kato, R.]]		[[Category: Kato, R]]
	[[Category: Nagae, M.]]		[[Category: Nagae, M]]
	[[Category: Tsuchiya, A.]]		[[Category: Tsuchiya, A]]
	[[Category: Wakatsuki, S.]]		[[Category: Wakatsuki, S]]
	[[Category: Yamamoto, K.]]		[[Category: Yamamoto, K]]
	[[Category: Fucosidase]]		[[Category: Fucosidase]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 01:21, 30 September 2014

2014-09-30T01:21:18Z

← Older revision		Revision as of 01:21, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2eac~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin==
			<StructureSection load='2eac' size='340' side='right' caption='[[2eac]], [[Resolution\|resolution]] 2.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAC FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DFU:(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL'>DFU</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eab\|2eab]], [[2ead\|2ead]], [[2eae\|2eae]], [[2eaf\|2eaf]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </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=2eac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eac OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eac RCSB], [http://www.ebi.ac.uk/pdbsum/2eac 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/ea/2eac_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 ==
			1,2-alpha-L-fucosidase (AfcA), which hydrolyzes the glycosidic linkage of Fucalpha1-2Gal via an inverting mechanism, was recently isolated from Bifidobacterium bifidum and classified as the first member of the novel glycoside hydrolase family 95. To better understand the molecular mechanism of this enzyme, we determined the x-ray crystal structures of the AfcA catalytic (Fuc) domain in unliganded and complexed forms with deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain is composed of four regions, an N-terminal beta region, a helical linker, an (alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this arrangement is similar to bacterial phosphorylases. In the complex structures, the ligands were buried in the central cavity of the helical barrel domain. Structural analyses in combination with mutational experiments revealed that the highly conserved Glu566 probably acts as a general acid catalyst. However, no carboxylic acid residue is found at the appropriate position for a general base catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound complex is suitably located to perform a nucleophilic attack on the C1 atom of L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical near the O1 atom of beta-L-fucose in the products-bound complex. Based on these data, we propose and discuss a novel catalytic reaction mechanism of AfcA.

	~~{{STRUCTURE_2eac\| PDB=2eac \| SCENE= }}~~		Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.,Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:17459873<ref>PMID:17459873</ref>

	~~===Crystal structure of 1~~,2-a~~-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17459873}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2eac]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017459873<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: 1,2-alpha-L-fucosidase]]		[[Category: 1,2-alpha-L-fucosidase]]
	[[Category: Bifidobacterium bifidum]]		[[Category: Bifidobacterium bifidum]]

OCA: Protected "2eac" [edit=sysop:move=sysop]

2013-01-06T10:36:09Z

Protected "2eac" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:36, 6 January 2013
(No difference)

OCA at 10:36, 6 January 2013

2013-01-06T10:36:06Z

← Older revision		Revision as of 10:36, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2eac.png\|left\|200px]]		[[Image:2eac.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2eac", 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_2eac\| PDB=2eac \| SCENE= }}		{{STRUCTURE_2eac\| PDB=2eac \| SCENE= }}

	===Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin===		===Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17459873}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17459873 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17459873}}		{{ABSTRACT_PUBMED_17459873}}

	==About this Structure==		==About this Structure==
	~~2EAC~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA].		[[2eac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17459873~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017459873</ref><references group="xtra"/>
	[[Category: 1,2-alpha-L-fucosidase]]		[[Category: 1,2-alpha-L-fucosidase]]
	[[Category: Bifidobacterium bifidum]]		[[Category: Bifidobacterium bifidum]]
Line 34:		Line 22:
	[[Category: Fucosidase]]		[[Category: Fucosidase]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
			[[Category: Hydrolase]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 00:52:39 2009''~~

OCA at 22:52, 17 February 2009

2009-02-17T22:52:40Z

← Older revision		Revision as of 22:52, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2EAC is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA].		2EAC is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAC OCA].

	==Reference==		==Reference==
	Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum., Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R, J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17459873 17459873]~~		<ref group="xtra">PMID:17459873</ref><references group="xtra"/>
	[[Category: 1,2-alpha-L-fucosidase]]		[[Category: 1,2-alpha-L-fucosidase]]
	[[Category: Bifidobacterium bifidum]]		[[Category: Bifidobacterium bifidum]]
	~~[[Category: Single protein]]~~
	[[Category: Katayama, T.]]		[[Category: Katayama, T.]]
	[[Category: Kato, R.]]		[[Category: Kato, R.]]
Line 36:		Line 35:
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 08~~:18:~~27 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:52:39 2009''