2exi - Revision history

OCA at 09:20, 14 February 2024

2024-02-14T09:20:12Z

←Older revision		Revision as of 09:20, 14 February 2024
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	<StructureSection load='2exi' size='340' side='right'caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='2exi' size='340' side='right'caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXI 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:~~2~~-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 2.15Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]~~</~~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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Xylan_1,4~~-~~beta~~-~~xylosidase Xylan 1,4~~-~~beta-xylosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37]~~ </~~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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [https://pdbe.org/2exi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [https://www.ebi.ac.uk/pdbsum/2exi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exi 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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [https://pdbe.org/2exi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [https://www.ebi.ac.uk/pdbsum/2exi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q09LX0_GEOSE Q09LX0_GEOSE]
	== 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=2exi 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=2exi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	beta-D-Xylosidases are glycoside hydrolases that catalyze the release of xylose units from short xylooligosaccharides and are engaged in the final breakdown of plant cell-wall hemicellulose. Here we describe the enzyme-substrate crystal structure of an inverting family 43 beta-xylosidase, from Geobacillus stearothermophilus T-6 (XynB3). Each XynB3 monomeric subunit is organized in two domains: an N-terminal five-bladed beta-propeller catalytic domain, and a beta-sandwich domain. The active site possesses a pocket topology, which is mainly constructed from the beta-propeller domain residues, and is closed on one side by a loop that originates from the beta-sandwich domain. This loop restricts the length of xylose units that can enter the active site, consistent with the exo mode of action of the enzyme. Structures of the enzyme-substrate (xylobiose) complex provide insights into the role of the three catalytic residues. The xylose moiety at the -1 subsite is held by a large number of hydrogen bonds, whereas only one hydroxyl of the xylose unit at the +1 subsite can create hydrogen bonds with the enzyme. The general base, Asp15, is located on the alpha-side of the -1 xylose sugar ring, 5.2 Angstroms from the anomeric carbon. This location enables it to activate a water molecule for a single-displacement attack on the anomeric carbon, resulting in inversion of the anomeric configuration. Glu187, the general acid, is 2.4 Angstroms from the glycosidic oxygen atom and can protonate the leaving aglycon. The third catalytic carboxylic acid, Asp128, is 4 Angstroms from the general acid; modulating its pK(a) and keeping it in the correct orientation relative to the substrate. In addition, Asp128 plays an important role in substrate binding via the 2-O of the glycon, which is important for the transition-state stabilization. Taken together, these key roles explain why Asp128 is an invariant among all five-bladed beta-propeller glycoside hydrolases.
-
-	The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues.,Brux C, Ben-David A, Shallom-Shezifi D, Leon M, Niefind K, Shoham G, Shoham Y, Schomburg D J Mol Biol. 2006 May 26;359(1):97-109. Epub 2006 Mar 20. PMID:16631196<ref>PMID:16631196</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2exi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Xylosidase 3D structures\|Xylosidase 3D structures]]		*[[Xylosidase 3D structures\|Xylosidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Xylan 1,4-beta-xylosidase]]~~	+	[[Category: Brux C]]
-	[[Category: Brux, C]]	+	[[Category: Niefind K]]
-	[[Category: Niefind, K]]	+	[[Category: Schomburg D]]
-	[[Category: Schomburg, D]]	+	[[Category: Shallom-Shezifi D]]
-	[[Category: Shallom-Shezifi, D]]	+	[[Category: Shoham Y]]
-	[[Category: Shoham, Y]]	+
-	~~[[Category: Family43]]~~	+
-	~~[[Category: Glykosidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolsase]]~~	+
-	~~[[Category: Xylosidase~~]]	+

OCA at 09:51, 5 May 2021

2021-05-05T09:51:22Z

←Older revision		Revision as of 09:51, 5 May 2021
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	<StructureSection load='2exi' size='340' side='right'caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='2exi' size='340' side='right'caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2EXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXI 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [~~http~~://pdbe.org/2exi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2exi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2exi 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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [https://pdbe.org/2exi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [https://www.ebi.ac.uk/pdbsum/2exi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exi ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Xylosidase\|Xylosidase]]	+	*[[Xylosidase 3D structures\|Xylosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:31, 24 July 2019

2019-07-24T09:31:06Z

←Older revision		Revision as of 09:31, 24 July 2019
Line 1:		Line 1:

	==Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus==		==Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus==
-	<StructureSection load='2exi' size='340' side='right' caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='2exi' size='340' side='right'caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXI FirstGlance]. <br>
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/ex/2exi_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2exi_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 2exi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2exi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Xylosidase\|Xylosidase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
		+	[[Category: Large Structures]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]
	[[Category: Brux, C]]		[[Category: Brux, C]]

OCA at 07:30, 18 October 2017

2017-10-18T07:30:13Z

←Older revision		Revision as of 07:30, 18 October 2017
Line 1:		Line 1:
		+
	==Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus==		==Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus==
	<StructureSection load='2exi' size='340' side='right' caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='2exi' size='340' side='right' caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [http://pdbe.org/2exi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [http://www.ebi.ac.uk/pdbsum/2exi 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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [http://pdbe.org/2exi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [http://www.ebi.ac.uk/pdbsum/2exi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2exi ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=2exi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2exi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2exi" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Xylosidase\|Xylosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:49, 11 September 2015

2015-09-11T14:49:23Z

←Older revision		Revision as of 14:49, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2exi' size='340' side='right' caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='2exi' size='340' side='right' caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXI 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [http://www.ebi.ac.uk/pdbsum/2exi 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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [http://pdbe.org/2exi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [http://www.ebi.ac.uk/pdbsum/2exi 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 2exi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geobacillus stearothermophilus~~]]	+	[[Category: Atcc 12980]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]
	[[Category: Brux, C]]		[[Category: Brux, C]]

OCA at 18:26, 15 January 2015

2015-01-15T18:26:24Z

←Older revision		Revision as of 18:26, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXI 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [http://www.ebi.ac.uk/pdbsum/2exi 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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [http://www.ebi.ac.uk/pdbsum/2exi 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 35:		Line 35:
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]
-	[[Category: Brux, C.]]	+	[[Category: Brux, C]]
-	[[Category: Niefind, K.]]	+	[[Category: Niefind, K]]
-	[[Category: Schomburg, D.]]	+	[[Category: Schomburg, D]]
-	[[Category: Shallom-Shezifi, D.]]	+	[[Category: Shallom-Shezifi, D]]
-	[[Category: Shoham, Y.]]	+	[[Category: Shoham, Y]]
	[[Category: Family43]]		[[Category: Family43]]
	[[Category: Glykosidase]]		[[Category: Glykosidase]]

OCA at 01:19, 30 September 2014

2014-09-30T01:19:01Z

←Older revision		Revision as of 01:19, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2exi.~~png~~\|~~left~~\|200px]]	+	==Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus==
		+	<StructureSection load='2exi' size='340' side='right' caption='[[2exi]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXI 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exh\|2exh]], [[2exj\|2exj]], [[2exk\|2exk]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </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=2exi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2exi RCSB], [http://www.ebi.ac.uk/pdbsum/2exi 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/ex/2exi_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 ==
		+	beta-D-Xylosidases are glycoside hydrolases that catalyze the release of xylose units from short xylooligosaccharides and are engaged in the final breakdown of plant cell-wall hemicellulose. Here we describe the enzyme-substrate crystal structure of an inverting family 43 beta-xylosidase, from Geobacillus stearothermophilus T-6 (XynB3). Each XynB3 monomeric subunit is organized in two domains: an N-terminal five-bladed beta-propeller catalytic domain, and a beta-sandwich domain. The active site possesses a pocket topology, which is mainly constructed from the beta-propeller domain residues, and is closed on one side by a loop that originates from the beta-sandwich domain. This loop restricts the length of xylose units that can enter the active site, consistent with the exo mode of action of the enzyme. Structures of the enzyme-substrate (xylobiose) complex provide insights into the role of the three catalytic residues. The xylose moiety at the -1 subsite is held by a large number of hydrogen bonds, whereas only one hydroxyl of the xylose unit at the +1 subsite can create hydrogen bonds with the enzyme. The general base, Asp15, is located on the alpha-side of the -1 xylose sugar ring, 5.2 Angstroms from the anomeric carbon. This location enables it to activate a water molecule for a single-displacement attack on the anomeric carbon, resulting in inversion of the anomeric configuration. Glu187, the general acid, is 2.4 Angstroms from the glycosidic oxygen atom and can protonate the leaving aglycon. The third catalytic carboxylic acid, Asp128, is 4 Angstroms from the general acid; modulating its pK(a) and keeping it in the correct orientation relative to the substrate. In addition, Asp128 plays an important role in substrate binding via the 2-O of the glycon, which is important for the transition-state stabilization. Taken together, these key roles explain why Asp128 is an invariant among all five-bladed beta-propeller glycoside hydrolases.

-	~~{{STRUCTURE_2exi\| PDB=2exi \| SCENE= }}~~	+	The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues.,Brux C, Ben-David A, Shallom-Shezifi D, Leon M, Niefind K, Shoham G, Shoham Y, Schomburg D J Mol Biol. 2006 May 26;359(1):97-109. Epub 2006 Mar 20. PMID:16631196<ref>PMID:16631196</ref>

-	~~===Structure~~ of the ~~family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_16631196}}~~	+	==See Also==
-		+	*[[Xylosidase\|Xylosidase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2exi~~]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:016631196<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]

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

2013-01-07T13:57:35Z

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

←Older revision

Revision as of 13:57, 7 January 2013

OCA at 13:57, 7 January 2013

2013-01-07T13:57:33Z

←Older revision		Revision as of 13:57, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2exi.png\|left\|200px]]		[[Image:2exi.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2exi", 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_2exi\| PDB=2exi \| SCENE= }}		{{STRUCTURE_2exi\| PDB=2exi \| SCENE= }}

	===Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus===		===Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16631196}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16631196 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16631196}}		{{ABSTRACT_PUBMED_16631196}}

	==About this Structure==		==About this Structure==
-	~~2EXI~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA].	+	[[2exi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16631196~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016631196</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]
Line 33:		Line 21:
	[[Category: Family43]]		[[Category: Family43]]
	[[Category: Glykosidase]]		[[Category: Glykosidase]]
		+	[[Category: Hydrolase]]
	[[Category: Hydrolsase]]		[[Category: Hydrolsase]]
	[[Category: Xylosidase]]		[[Category: Xylosidase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:50:39 2009''

OCA at 22:50, 17 February 2009

2009-02-17T22:50:41Z

←Older revision		Revision as of 22:50, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2EXI is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA].	+	2EXI is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXI OCA].

	==Reference==		==Reference==
-	The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues., Brux C, Ben-David A, Shallom-Shezifi D, Leon M, Niefind K, Shoham G, Shoham Y, Schomburg D, J Mol Biol. 2006 May 26;359(1):97-109. Epub 2006 Mar 20. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16631196 16631196]~~	+	<ref group="xtra">PMID:16631196</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Single protein]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]
	[[Category: Brux, C.]]		[[Category: Brux, C.]]
Line 37:		Line 36:
	[[Category: Xylosidase]]		[[Category: Xylosidase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 08~~:16:~~09 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:50:39 2009''