1bvv - Revision history

OCA at 15:36, 13 March 2024

OCA — Wed, 13 Mar 2024 15:36:38 GMT

←Older revision		Revision as of 15:36, 13 March 2024
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	<StructureSection load='1bvv' size='340' side='right'caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1bvv' size='340' side='right'caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_24 Atcc 24~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BVV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BVV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DFX:1,2~~-~~DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>~~, ~~<scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.8Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Endo-~~1,4-~~beta~~-~~xylanase Endo~~-~~1,4~~-~~beta-xylanase]~~, ~~with EC number [https~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [https://pdbe.org/1bvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [https://www.ebi.ac.uk/pdbsum/1bvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvv 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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [https://pdbe.org/1bvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [https://www.ebi.ac.uk/pdbsum/1bvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYNA_NIACI XYNA_NIACI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 20:
	</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=1bvv 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=1bvv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The 1.8 A resolution structure of the glycosyl-enzyme intermediate formed on the retaining beta-1,4-xylanase from Bacillus circulans has been determined using X-ray crystallographic techniques. The 2-fluoro-xylose residue bound in the -1 subsite adopts a 2,5B (boat) conformation, allowing atoms C5, O5, C1, and C2 of the sugar to achieve coplanarity as required at the oxocarbenium ion-like transition states of the double-displacement catalytic mechanism. Comparison of this structure to that of a mutant of this same enzyme noncovalently complexed with xylotetraose [Wakarchuk et al. (1994) Protein Sci. 3, 467-475] reveals a number of differences beyond the distortion of the sugar moiety. Most notably, a bifurcated hydrogen bond interaction is formed in the glycosyl-enzyme intermediate involving Heta of Tyr69, the endocyclic oxygen (O5) of the xylose residue in the -1 subsite, and Oepsilon2 of the catalytic nucleophile, Glu78. To gain additional understanding of the role of Tyr69 at the active site of this enzyme, we also determined the 1.5 A resolution structure of the catalytically inactive Tyr69Phe mutant. Interestingly, no significant structural perturbation due to the loss of the phenolic group is observed. These results suggest that the interactions involving the phenolic group of Tyr69, O5 of the proximal saccharide, and Glu78 Oepsilon2 are important for the catalytic mechanism of this enzyme, and it is proposed that, through charge redistribution, these interactions serve to stabilize the oxocarbenium-like ion of the transition state. Studies of the covalent glycosyl-enzyme intermediate of this xylanase also provide insight into specificity, as contacts with C5 of the xylose moiety exclude sugars with hydroxymethyl substituents, and the mechanism of catalysis, including aspects of stereoelectronic theory as applied to glycoside hydrolysis.
-
-	Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.,Sidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD Biochemistry. 1999 Apr 27;38(17):5346-54. PMID:10220321<ref>PMID:10220321</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1bvv" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 24]]
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Brayer, G D~~]]	+	[[Category: Niallia circulans]]
-	[[Category: ~~Sidhu, G~~]]	+	[[Category: Brayer GD]]
-	[[Category: ~~Boat conformation]]~~	+	[[Category: Sidhu G]]
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Glycosyl-enzyme intermediate]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Xylan degradation]]~~	+
-	~~[[Category: Xylanase~~]]	+

OCA at 10:30, 14 July 2021

OCA — Wed, 14 Jul 2021 10:30:26 GMT

←Older revision		Revision as of 10:30, 14 July 2021
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	<StructureSection load='1bvv' size='340' side='right'caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1bvv' size='340' side='right'caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BVV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BVV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [~~http~~://pdbe.org/1bvv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bvv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvv 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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [https://pdbe.org/1bvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [https://www.ebi.ac.uk/pdbsum/1bvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:14, 10 October 2019

OCA — Thu, 10 Oct 2019 07:14:44 GMT

←Older revision		Revision as of 07:14, 10 October 2019
Line 1:		Line 1:

	==SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE==		==SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE==
-	<StructureSection load='1bvv' size='340' side='right' caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1bvv' size='340' side='right'caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BVV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BVV FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/1bvv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/1bvv_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 33:		Line 33:
	[[Category: Atcc 24]]		[[Category: Atcc 24]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Brayer, G D]]		[[Category: Brayer, G D]]
	[[Category: Sidhu, G]]		[[Category: Sidhu, G]]

OCA at 08:10, 29 November 2017

OCA — Wed, 29 Nov 2017 08:10:01 GMT

←Older revision		Revision as of 08:10, 29 November 2017
Line 1:		Line 1:
		+
	==SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE==		==SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE==
	<StructureSection load='1bvv' size='340' side='right' caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1bvv' size='340' side='right' caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [http://pdbe.org/1bvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [http://www.ebi.ac.uk/pdbsum/1bvv 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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [http://pdbe.org/1bvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [http://www.ebi.ac.uk/pdbsum/1bvv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 11:54, 8 February 2016

OCA — Mon, 08 Feb 2016 11:54:53 GMT

←Older revision		Revision as of 11:54, 8 February 2016
Line 15:		Line 15:
	<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=1bvv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:20, 10 September 2015

OCA — Thu, 10 Sep 2015 11:20:08 GMT

←Older revision		Revision as of 11:20, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1bvv' size='340' side='right' caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1bvv' size='340' side='right' caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_circulans Bacillus circulans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BVV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BVV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [http://www.ebi.ac.uk/pdbsum/1bvv 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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [http://pdbe.org/1bvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [http://www.ebi.ac.uk/pdbsum/1bvv PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1bvv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus circulans~~]]	+	[[Category: Atcc 24]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Brayer, G D]]		[[Category: Brayer, G D]]

OCA at 10:07, 22 December 2014

OCA — Mon, 22 Dec 2014 10:07:28 GMT

←Older revision		Revision as of 10:07, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BVV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BVV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [http://www.ebi.ac.uk/pdbsum/1bvv 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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [http://www.ebi.ac.uk/pdbsum/1bvv 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 31:		Line 31:
	[[Category: Bacillus circulans]]		[[Category: Bacillus circulans]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: Brayer, G D.]]	+	[[Category: Brayer, G D]]
-	[[Category: Sidhu, G.]]	+	[[Category: Sidhu, G]]
	[[Category: Boat conformation]]		[[Category: Boat conformation]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]

OCA at 09:40, 13 August 2014

OCA — Wed, 13 Aug 2014 09:40:31 GMT

←Older revision		Revision as of 09:40, 13 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1bvv.~~png\|left~~\|200px]]	+	==SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE==
		+	<StructureSection load='1bvv' size='340' side='right' caption='[[1bvv]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BVV FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [http://www.ebi.ac.uk/pdbsum/1bvv 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/bv/1bvv_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 ==
		+	The 1.8 A resolution structure of the glycosyl-enzyme intermediate formed on the retaining beta-1,4-xylanase from Bacillus circulans has been determined using X-ray crystallographic techniques. The 2-fluoro-xylose residue bound in the -1 subsite adopts a 2,5B (boat) conformation, allowing atoms C5, O5, C1, and C2 of the sugar to achieve coplanarity as required at the oxocarbenium ion-like transition states of the double-displacement catalytic mechanism. Comparison of this structure to that of a mutant of this same enzyme noncovalently complexed with xylotetraose [Wakarchuk et al. (1994) Protein Sci. 3, 467-475] reveals a number of differences beyond the distortion of the sugar moiety. Most notably, a bifurcated hydrogen bond interaction is formed in the glycosyl-enzyme intermediate involving Heta of Tyr69, the endocyclic oxygen (O5) of the xylose residue in the -1 subsite, and Oepsilon2 of the catalytic nucleophile, Glu78. To gain additional understanding of the role of Tyr69 at the active site of this enzyme, we also determined the 1.5 A resolution structure of the catalytically inactive Tyr69Phe mutant. Interestingly, no significant structural perturbation due to the loss of the phenolic group is observed. These results suggest that the interactions involving the phenolic group of Tyr69, O5 of the proximal saccharide, and Glu78 Oepsilon2 are important for the catalytic mechanism of this enzyme, and it is proposed that, through charge redistribution, these interactions serve to stabilize the oxocarbenium-like ion of the transition state. Studies of the covalent glycosyl-enzyme intermediate of this xylanase also provide insight into specificity, as contacts with C5 of the xylose moiety exclude sugars with hydroxymethyl substituents, and the mechanism of catalysis, including aspects of stereoelectronic theory as applied to glycoside hydrolysis.

-	~~{{STRUCTURE_1bvv\| PDB=1bvv \| SCENE= }}~~	+	Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.,Sidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD Biochemistry. 1999 Apr 27;38(17):5346-54. PMID:10220321<ref>PMID:10220321</ref>

-	~~===SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G~~/~~11 XYLANASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10220321}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1bvv]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_circulans Bacillus circulans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010220321<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus circulans]]		[[Category: Bacillus circulans]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]

OCA: Protected "1bvv" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 20:39:05 GMT

Protected "1bvv" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:39, 21 October 2012

OCA at 20:39, 21 October 2012

OCA — Sun, 21 Oct 2012 20:39:01 GMT

←Older revision		Revision as of 20:39, 21 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1bvv.png\|left\|200px]]		[[Image:1bvv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1bvv", 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_1bvv\| PDB=1bvv \| SCENE= }}		{{STRUCTURE_1bvv\| PDB=1bvv \| SCENE= }}

	===SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE===		===SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10220321}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10220321 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10220321}}		{{ABSTRACT_PUBMED_10220321}}

	==About this Structure==		==About this Structure==
-	~~1BVV~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA].	+	[[1bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10220321~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010220321</ref><references group="xtra"/>
	[[Category: Bacillus circulans]]		[[Category: Bacillus circulans]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
Line 34:		Line 22:
	[[Category: Xylan degradation]]		[[Category: Xylan degradation]]
	[[Category: Xylanase]]		[[Category: Xylanase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:48:30 2009''