2d73 - Revision history

OCA at 13:46, 13 March 2024

2024-03-13T13:46:57Z

←Older revision		Revision as of 13:46, 13 March 2024
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	<StructureSection load='2d73' size='340' side='right'caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d73' size='340' side='right'caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D73 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D73 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>~~</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]] 1.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SusB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~226186 BACTN])</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></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20]~~ </~~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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [https://pdbe.org/2d73 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [https://www.ebi.ac.uk/pdbsum/2d73 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d73 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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [https://pdbe.org/2d73 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [https://www.ebi.ac.uk/pdbsum/2d73 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d73 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SUSB_BACTN SUSB_BACTN] Glucoamylase that hydrolyzes alpha-1,4-glucosidic linkages, alpha-1,6-, alpha-1,3- and alpha-1,2-glucosidic linkages during starch degradation.<ref>PMID:8955399</ref> <ref>PMID:18981178</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d73 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=2d73 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	SusB, an 84-kDa alpha-glucoside hydrolase involved in the starch utilization system (sus) of Bacteroides thetaiotaomicron, belongs to glycoside hydrolase (GH) family 97. We have determined the enzymatic characteristics and the crystal structures in free and acarbose-bound form at 1.6A resolution. SusB hydrolyzes the alpha-glucosidic linkage, with inversion of anomeric configuration liberating the beta-anomer of glucose as the reaction product. The substrate specificity of SusB, hydrolyzing not only alpha-1,4-glucosidic linkages but also alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages, is clearly different from other well known glucoamylases belonging to GH15. The structure of SusB was solved by the single-wavelength anomalous diffraction method with sulfur atoms as anomalous scatterers using an in-house x-ray source. SusB includes three domains as follows: the N-terminal, catalytic, and C-terminal domains. The structure of the SusB-acarbose complex shows a constellation of carboxyl groups at the catalytic center; Glu532 is positioned to provide protonic assistance to leaving group departure, with Glu439 and Glu508 both positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water. A structural comparison with other glycoside hydrolases revealed significant similarity between the catalytic domain of SusB and those of alpha-retaining glycoside hydrolases belonging to GH27, -36, and -31 despite the differences in catalytic mechanism. SusB and the other retaining enzymes appear to have diverged from a common ancestor and individually acquired the functional carboxyl groups during the process of evolution. Furthermore, sequence comparison of the active site based on the structure of SusB indicated that GH97 included both retaining and inverting enzymes.
-
-	Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.,Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M J Biol Chem. 2008 Dec 26;283(52):36328-37. Epub 2008 Nov 3. PMID:18981178<ref>PMID:18981178</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2d73" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alpha~~-~~glucosidase]]~~	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-	~~[[Category: Bactn~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kitamura, M]]	+	[[Category: Kitamura M]]
-	[[Category: Yao, M]]	+	[[Category: Yao M]]
-	~~[[Category: Glycoside hydrolase family 97]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 11:54, 3 February 2021

2021-02-03T11:54:53Z

←Older revision		Revision as of 11:54, 3 February 2021
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	==Crystal Structure Analysis of SusB==		==Crystal Structure Analysis of SusB==
-	<StructureSection load='2d73' size='340' side='right' caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2d73' size='340' side='right'caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D73 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D73 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></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></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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-glucosidase Alpha-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [~~http~~://pdbe.org/2d73 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d73 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d73 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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [https://pdbe.org/2d73 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [https://www.ebi.ac.uk/pdbsum/2d73 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d73 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d73_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d73_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 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2d73" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2d73" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	[[Category: Alpha-glucosidase]]		[[Category: Alpha-glucosidase]]
	[[Category: Bactn]]		[[Category: Bactn]]
		+	[[Category: Large Structures]]
	[[Category: Kitamura, M]]		[[Category: Kitamura, M]]
	[[Category: Yao, M]]		[[Category: Yao, M]]

OCA at 14:40, 12 October 2017

2017-10-12T14:40:51Z

←Older revision		Revision as of 14:40, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure Analysis of SusB==		==Crystal Structure Analysis of SusB==
	<StructureSection load='2d73' size='340' side='right' caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d73' size='340' side='right' caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [http://pdbe.org/2d73 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [http://www.ebi.ac.uk/pdbsum/2d73 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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [http://pdbe.org/2d73 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [http://www.ebi.ac.uk/pdbsum/2d73 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d73 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2d73" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2d73" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Alpha-glucosidase\|Alpha-glucosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:29, 9 February 2016

2016-02-09T10:29:52Z

←Older revision		Revision as of 10:29, 9 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d73 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:23, 10 September 2015

2015-09-10T21:23:00Z

←Older revision		Revision as of 21:23, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2d73' size='340' side='right' caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d73' size='340' side='right' caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacteroides_thetaiotaomicron_vpi-5482 Bacteroides thetaiotaomicron vpi-5482~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D73 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D73 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></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></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 ~~Bacteroides thetaiotaomicron VPI-5482~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [http://www.ebi.ac.uk/pdbsum/2d73 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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [http://pdbe.org/2d73 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [http://www.ebi.ac.uk/pdbsum/2d73 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 2d73" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alpha-glucosidase\|Alpha-glucosidase]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Alpha-glucosidase]]		[[Category: Alpha-glucosidase]]
-	[[Category: ~~Bacteroides thetaiotaomicron vpi-5482~~]]	+	[[Category: Bactn]]
	[[Category: Kitamura, M]]		[[Category: Kitamura, M]]
	[[Category: Yao, M]]		[[Category: Yao, M]]

OCA at 17:19, 15 January 2015

2015-01-15T17:19:01Z

←Older revision		Revision as of 17:19, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_vpi-5482 Bacteroides thetaiotaomicron vpi-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D73 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_vpi-5482 Bacteroides thetaiotaomicron vpi-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D73 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 Bacteroides thetaiotaomicron VPI-5482])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 Bacteroides thetaiotaomicron VPI-5482])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [http://www.ebi.ac.uk/pdbsum/2d73 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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [http://www.ebi.ac.uk/pdbsum/2d73 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: Alpha-glucosidase]]		[[Category: Alpha-glucosidase]]
	[[Category: Bacteroides thetaiotaomicron vpi-5482]]		[[Category: Bacteroides thetaiotaomicron vpi-5482]]
-	[[Category: Kitamura, M.]]	+	[[Category: Kitamura, M]]
-	[[Category: Yao, M.]]	+	[[Category: Yao, M]]
	[[Category: Glycoside hydrolase family 97]]		[[Category: Glycoside hydrolase family 97]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 02:16, 30 September 2014

2014-09-30T02:16:28Z

←Older revision		Revision as of 02:16, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2d73.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure Analysis of SusB==
		+	<StructureSection load='2d73' size='340' side='right' caption='[[2d73]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2d73]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_vpi-5482 Bacteroides thetaiotaomicron vpi-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D73 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SusB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 Bacteroides thetaiotaomicron VPI-5482])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=2d73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d73 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d73 RCSB], [http://www.ebi.ac.uk/pdbsum/2d73 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/d7/2d73_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 ==
		+	SusB, an 84-kDa alpha-glucoside hydrolase involved in the starch utilization system (sus) of Bacteroides thetaiotaomicron, belongs to glycoside hydrolase (GH) family 97. We have determined the enzymatic characteristics and the crystal structures in free and acarbose-bound form at 1.6A resolution. SusB hydrolyzes the alpha-glucosidic linkage, with inversion of anomeric configuration liberating the beta-anomer of glucose as the reaction product. The substrate specificity of SusB, hydrolyzing not only alpha-1,4-glucosidic linkages but also alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages, is clearly different from other well known glucoamylases belonging to GH15. The structure of SusB was solved by the single-wavelength anomalous diffraction method with sulfur atoms as anomalous scatterers using an in-house x-ray source. SusB includes three domains as follows: the N-terminal, catalytic, and C-terminal domains. The structure of the SusB-acarbose complex shows a constellation of carboxyl groups at the catalytic center; Glu532 is positioned to provide protonic assistance to leaving group departure, with Glu439 and Glu508 both positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water. A structural comparison with other glycoside hydrolases revealed significant similarity between the catalytic domain of SusB and those of alpha-retaining glycoside hydrolases belonging to GH27, -36, and -31 despite the differences in catalytic mechanism. SusB and the other retaining enzymes appear to have diverged from a common ancestor and individually acquired the functional carboxyl groups during the process of evolution. Furthermore, sequence comparison of the active site based on the structure of SusB indicated that GH97 included both retaining and inverting enzymes.

-	~~{{STRUCTURE_2d73\| PDB=2d73 \| SCENE= }}~~	+	Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.,Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M J Biol Chem. 2008 Dec 26;283(52):36328-37. Epub 2008 Nov 3. PMID:18981178<ref>PMID:18981178</ref>

-	~~===Crystal Structure Analysis~~ of ~~SusB===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18981178}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2d73]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacteroides_thetaiotaomicron_vpi-5482 Bacteroides thetaiotaomicron vpi-5482]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018981178<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alpha-glucosidase]]		[[Category: Alpha-glucosidase]]
	[[Category: Bacteroides thetaiotaomicron vpi-5482]]		[[Category: Bacteroides thetaiotaomicron vpi-5482]]

OCA: Protected "2d73" [edit=sysop:move=sysop]

2013-01-06T11:29:21Z

Protected "2d73" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:29, 6 January 2013

OCA at 11:29, 6 January 2013

2013-01-06T11:29:18Z

←Older revision		Revision as of 11:29, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2d73.png\|left\|200px]]		[[Image:2d73.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2d73", 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_2d73\| PDB=2d73 \| SCENE= }}		{{STRUCTURE_2d73\| PDB=2d73 \| SCENE= }}

	===Crystal Structure Analysis of SusB===		===Crystal Structure Analysis of SusB===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18981178}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18981178 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18981178}}		{{ABSTRACT_PUBMED_18981178}}

	==About this Structure==		==About this Structure==
-	~~2D73~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Bacteria Bacteria~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA].	+	[[2d73]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_vpi-5482 Bacteroides thetaiotaomicron vpi-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18981178~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018981178</ref><references group="xtra"/>
	[[Category: Alpha-glucosidase]]		[[Category: Alpha-glucosidase]]
-	[[Category: ~~Bacteria~~]]	+	[[Category: Bacteroides thetaiotaomicron vpi-5482]]
	[[Category: Kitamura, M.]]		[[Category: Kitamura, M.]]
	[[Category: Yao, M.]]		[[Category: Yao, M.]]
	[[Category: Glycoside hydrolase family 97]]		[[Category: Glycoside hydrolase family 97]]
		+	[[Category: Hydrolase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:55:40 2009''

OCA at 17:55, 22 July 2009

2009-07-22T17:55:42Z

←Older revision		Revision as of 17:55, 22 July 2009
Line 12:		Line 12:
	===Crystal Structure Analysis of SusB===		===Crystal Structure Analysis of SusB===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18981178}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18981178 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18981178}}

	==About this Structure==		==About this Structure==
	2D73 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA].		2D73 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D73 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:18981178</ref><references group="xtra"/>
	[[Category: Alpha-glucosidase]]		[[Category: Alpha-glucosidase]]
	[[Category: Bacteria]]		[[Category: Bacteria]]
Line 22:		Line 31:
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 09~~:09:06 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:55:40 2009''