2d0f - Revision history

OCA at 11:33, 22 May 2024

2024-05-22T11:33:02Z

← Older revision		Revision as of 11:33, 22 May 2024
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	<StructureSection load='2d0f' size='340' side='right'caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2d0f' size='340' side='right'caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43649 Atcc 43649~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.08Å</td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</div>~~</~~td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PRD_900065:beta-maltotriose'>PRD_900065</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [https://pdbe.org/2d0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [https://www.ebi.ac.uk/pdbsum/2d0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0f 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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [https://pdbe.org/2d0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [https://www.ebi.ac.uk/pdbsum/2d0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU]] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.		[https://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.
	== 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: Alpha-amylase]]~~
	~~[[Category: Atcc 43649]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Abe, A]]		[[Category: Thermoactinomyces vulgaris]]
	[[Category: Kamitori, S]]		[[Category: Abe A]]
	[[Category: Sakano, Y]]		[[Category: Kamitori S]]
	[[Category: Tonozuka, T]]		[[Category: Sakano Y]]
	[[Category: Yoshida, H]]		[[Category: Tonozuka T]]
	~~[[Category: Hydrolase~~]]		[[Category: Yoshida H]]

OCA at 06:47, 10 November 2021

2021-11-10T06:47:51Z

← Older revision		Revision as of 06:47, 10 November 2021
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	<StructureSection load='2d0f' size='340' side='right'caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2d0f' size='340' side='right'caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D0F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [~~http~~://pdbe.org/2d0f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d0f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0f 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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [https://pdbe.org/2d0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [https://www.ebi.ac.uk/pdbsum/2d0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU]] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.		[[https://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU]] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:00, 4 March 2020

2020-03-04T08:00:22Z

← Older revision		Revision as of 08:00, 4 March 2020
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	==Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide==		==Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide==
	<StructureSection load='2d0f' size='340' side='right' caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2d0f' size='340' side='right'caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0F FirstGlance]. <br>
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	==See Also==		==See Also==
	*[[Amylase\|Amylase]]		*[[Amylase 3D structures\|Amylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Atcc 43649]]		[[Category: Atcc 43649]]
			[[Category: Large Structures]]
	[[Category: Abe, A]]		[[Category: Abe, A]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]

OCA at 06:55, 30 May 2018

2018-05-30T06:55:11Z

← Older revision		Revision as of 06:55, 30 May 2018
Line 1:		Line 1:

	==Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide==		==Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide==
	<StructureSection load='2d0f' size='340' side='right' caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2d0f' size='340' side='right' caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://pdbe.org/2d0f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [http://www.ebi.ac.uk/pdbsum/2d0f 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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://pdbe.org/2d0f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [http://www.ebi.ac.uk/pdbsum/2d0f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/d0/2d0f_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/2d0f_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>
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	==See Also==		==See Also==
	*[[Amylase\|Amylase]]		*[[Amylase\|Amylase]]
	*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:42, 9 February 2016

2016-02-09T08:42:50Z

← Older revision		Revision as of 08:42, 9 February 2016
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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=2d0f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:33, 10 September 2015

2015-09-10T20:33:29Z

← Older revision		Revision as of 20:33, 10 September 2015
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	<StructureSection load='2d0f' size='340' side='right' caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2d0f' size='340' side='right' caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermoactinomyces_vulgaris Thermoactinomyces vulgaris~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [http://www.ebi.ac.uk/pdbsum/2d0f 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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://pdbe.org/2d0f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [http://www.ebi.ac.uk/pdbsum/2d0f PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 2d0f" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: ~~Thermoactinomyces vulgaris~~]]		[[Category: Atcc 43649]]
	[[Category: Abe, A]]		[[Category: Abe, A]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]

OCA at 05:48, 25 December 2014

2014-12-25T05:48:03Z

← Older revision		Revision as of 05:48, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0F FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [http://www.ebi.ac.uk/pdbsum/2d0f 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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [http://www.ebi.ac.uk/pdbsum/2d0f PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU]] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	==See Also==		==See Also==
	*[[Amylase\|Amylase]]		*[[Amylase\|Amylase]]
			*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Thermoactinomyces vulgaris]]		[[Category: Thermoactinomyces vulgaris]]
	[[Category: Abe, A.]]		[[Category: Abe, A]]
	[[Category: Kamitori, S.]]		[[Category: Kamitori, S]]
	[[Category: Sakano, Y.]]		[[Category: Sakano, Y]]
	[[Category: Tonozuka, T.]]		[[Category: Tonozuka, T]]
	[[Category: Yoshida, H~~.]]~~		[[Category: Yoshida, H]]
	~~[[Category: Alpha-amylase~~]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 05:26, 29 September 2014

2014-09-29T05:26:43Z

← Older revision		Revision as of 05:26, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2d0f~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide==
			<StructureSection load='2d0f' size='340' side='right' caption='[[2d0f]], [[Resolution\|resolution]] 2.08Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0F FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ji1\|1ji1]], [[2d0g\|2d0g]], [[2d0h\|2d0h]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </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=2d0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d0f RCSB], [http://www.ebi.ac.uk/pdbsum/2d0f 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/d0/2d0f_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 ==
			Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) has unique hydrolyzing activities for pullulan with sequence repeats of alpha-(1,4), alpha-(1,4), and alpha-(1,6) glycosidic linkages, as well as for starch. TVAI mainly hydrolyzes alpha-(1,4) glycosidic linkages to produce a panose, but it also hydrolyzes alpha-(1,6) glycosidic linkages with a lesser efficiency. X-ray structures of three complexes comprising an inactive mutant TVAI (D356N or D356N/E396Q) and a pullulan model oligosaccharide (P2; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]2 or P5; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]5) were determined. The complex D356N/P2 is a mimic of the enzyme/product complex in the main catalytic reaction of TVAI, and a structural comparison with Aspergillus oryzaealpha-amylase showed that the (-) subsites of TVAI are responsible for recognizing both starch and pullulan. D356N/E396Q/P2 and D356N/E396Q/P5 provided models of the enzyme/substrate complex recognizing the alpha-(1,6) glycosidic linkage at the hydrolyzing site. They showed that only subsites -1 and -2 at the nonreducing end of TVAI are effective in the hydrolysis of alpha-(1,6) glycosidic linkages, leading to weak interactions between substrates and the enzyme. Domain N of TVAI is a starch-binding domain acting as an anchor in the catalytic reaction of the enzyme. In this study, additional substrates were also found to bind to domain N, suggesting that domain N also functions as a pullulan-binding domain.

	~~{{STRUCTURE_2d0f\| PDB=2d0f \| SCENE= }}~~		Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages.,Abe A, Yoshida H, Tonozuka T, Sakano Y, Kamitori S FEBS J. 2005 Dec;272(23):6145-53. PMID:16302977<ref>PMID:16302977</ref>

	~~===Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2~~, a ~~pullulan model oligosaccharide===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16302977}}~~

	~~==About this Structure==~~
	~~[[2d0f]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA].~~

	==See Also==		==See Also==
	*[[~~Alpha-~~Amylase\|~~Alpha-~~Amylase]]		*[[Amylase\|Amylase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016302977<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Thermoactinomyces vulgaris]]		[[Category: Thermoactinomyces vulgaris]]

OCA at 13:18, 20 October 2012

2012-10-20T13:18:45Z

← Older revision		Revision as of 13:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2d0f]] is a 1 chain structure ~~of [[Alpha-Amylase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA].		[[2d0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0F OCA].

	==See Also==		==See Also==

OCA: Protected "2d0f" [edit=sysop:move=sysop]

2012-07-26T11:33:29Z

Protected "2d0f" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:33, 26 July 2012
(No difference)