1xys - Revision history

OCA at 08:54, 14 February 2024

OCA — Wed, 14 Feb 2024 08:54:03 GMT

←Older revision		Revision as of 08:54, 14 February 2024
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	<StructureSection load='1xys' size='340' side='right'caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1xys' size='340' side='right'caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XYS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYS 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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~155077~~ "~~Cellvibrio cellulosa~~" ~~Nagy et al. 2002])</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~~'>~~[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'>[https://proteopedia.org/fgij/fg.htm?mol=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [https://pdbe.org/1xys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [https://www.ebi.ac.uk/pdbsum/1xys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xys ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [~~http~~://pdbe.org/1xys PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xys PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xys ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYNA_CELJU XYNA_CELJU]
	== 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=1xys 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=1xys ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Sequence alignment suggests that xylanases evolved from two ancestral proteins and therefore can be grouped into two families, designated F and G. Family F enzymes show no sequence similarity with any known structure and their architecture is unknown. Studies of an inactive enzyme-substrate complex will help to elucidate the structural basis of binding and catalysis in the family F xylanases. RESULTS: We have therefore determined the crystal structure of the catalytic domain of a family F enzyme, Pseudomonas fluorescens subsp. cellulosa xylanase A, at 2.5 A resolution and a crystallographic R-factor of 0.20. The structure was solved using an engineered catalytic core in which the nucleophilic glutamate was replaced by a cysteine. As expected, this yielded both high-quality mercurial derivatives and an inactive enzyme which enabled the preparation of the inactive enzyme-substrate complex in the crystal. We show that family F xylanases are eight-fold alpha/beta-barrels (TIM barrels) with two active-site glutamates, one of which is the nucleophile and the other the acid-base. Xylopentaose binds to five subsites A-E with the cleaved bond between subsites D and E. Ca2+ binding, remote from the active-site glutamates, stabilizes the structure and may be involved in the binding of extended substrates. CONCLUSIONS: The architecture of P. fluorescens subsp. cellulosa has been determined crystallographically to be a commonly occurring enzyme fold, the eight-fold alpha/beta-barrel. Xylopentaose binds across the carboxy-terminal end of the alpha/beta-barrel in an active-site cleft which contains the two catalytic glutamates.
-
-	Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites.,Harris GW, Jenkins JA, Connerton I, Cummings N, Lo Leggio L, Scott M, Hazlewood GP, Laurie JI, Gilbert HJ, Pickersgill RW Structure. 1994 Nov 15;2(11):1107-16. PMID:7881909<ref>PMID:7881909</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1xys" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cellvibrio ~~cellulosa nagy et al. 2002]]~~	+	[[Category: Cellvibrio japonicus]]
-	~~[[Category: Endo-1,4-beta-xylanase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Connerton, I]]	+	[[Category: Connerton I]]
-	[[Category: Harris~~, G W~~]]	+	[[Category: Harris GW]]
-	[[Category: Jenkins~~, J A~~]]	+	[[Category: Jenkins JA]]
-	[[Category: Pickersgill~~, R W]]~~	+	[[Category: Pickersgill RW]]
-	~~[[Category: Family 10 of glycosyl-hydrolase]]~~	+
-	~~[[Category: Family f xylanase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:26, 6 January 2021

OCA — Wed, 06 Jan 2021 10:26:32 GMT

←Older revision		Revision as of 10:26, 6 January 2021
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	==CATALYTIC CORE OF XYLANASE A E246C MUTANT==		==CATALYTIC CORE OF XYLANASE A E246C MUTANT==
-	<StructureSection load='1xys' size='340' side='right' caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1xys' size='340' side='right'caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XYS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XYS 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">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 "Cellvibrio cellulosa" Nagy et al. 2002])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 "Cellvibrio cellulosa" Nagy et al. 2002])</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=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://pdbe.org/1xys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xys ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://pdbe.org/1xys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xys ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	[[Category: Cellvibrio cellulosa nagy et al. 2002]]		[[Category: Cellvibrio cellulosa nagy et al. 2002]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Connerton, I]]		[[Category: Connerton, I]]
	[[Category: Harris, G W]]		[[Category: Harris, G W]]

OCA at 07:39, 18 April 2018

OCA — Wed, 18 Apr 2018 07:39:22 GMT

←Older revision		Revision as of 07:39, 18 April 2018
Line 1:		Line 1:
		+
	==CATALYTIC CORE OF XYLANASE A E246C MUTANT==		==CATALYTIC CORE OF XYLANASE A E246C MUTANT==
	<StructureSection load='1xys' size='340' side='right' caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1xys' size='340' side='right' caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 "Cellvibrio cellulosa" Nagy et al. 2002])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 "Cellvibrio cellulosa" Nagy et al. 2002])</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=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://pdbe.org/1xys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys 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=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://pdbe.org/1xys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xys ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xy/1xys_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xy/1xys_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>

OCA at 12:24, 9 February 2016

OCA — Tue, 09 Feb 2016 12:24:45 GMT

←Older revision		Revision as of 12:24, 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=1xys ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:13, 10 September 2015

OCA — Thu, 10 Sep 2015 22:13:46 GMT

←Older revision		Revision as of 22:13, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1xys' size='340' side='right' caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1xys' size='340' side='right' caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Cellvibrio_japonicus Cellvibrio japonicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYS 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">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 Cellvibrio ~~japonicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 "Cellvibrio cellulosa" Nagy et al. 2002])</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=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys 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=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://pdbe.org/1xys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys 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 1xys" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cellvibrio ~~japonicus~~]]	+	[[Category: Cellvibrio cellulosa nagy et al. 2002]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Connerton, I]]		[[Category: Connerton, I]]

OCA at 10:44, 8 January 2015

OCA — Thu, 08 Jan 2015 10:44:57 GMT

←Older revision		Revision as of 10:44, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYS 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">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 Cellvibrio japonicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 Cellvibrio japonicus])</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=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys 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=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys 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: Cellvibrio japonicus]]		[[Category: Cellvibrio japonicus]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: Connerton, I.]]	+	[[Category: Connerton, I]]
-	[[Category: Harris, G W.]]	+	[[Category: Harris, G W]]
-	[[Category: Jenkins, J A.]]	+	[[Category: Jenkins, J A]]
-	[[Category: Pickersgill, R W.]]	+	[[Category: Pickersgill, R W]]
	[[Category: Family 10 of glycosyl-hydrolase]]		[[Category: Family 10 of glycosyl-hydrolase]]
	[[Category: Family f xylanase]]		[[Category: Family f xylanase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 22:06, 29 September 2014

OCA — Mon, 29 Sep 2014 22:06:28 GMT

←Older revision		Revision as of 22:06, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xys.~~png~~\|~~left~~\|200px]]	+	==CATALYTIC CORE OF XYLANASE A E246C MUTANT==
		+	<StructureSection load='1xys' size='340' side='right' caption='[[1xys]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYS 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">TRUNCATED XYNA (CODONS 264-611) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155077 Cellvibrio japonicus])</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xys RCSB], [http://www.ebi.ac.uk/pdbsum/1xys 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/xy/1xys_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 ==
		+	BACKGROUND: Sequence alignment suggests that xylanases evolved from two ancestral proteins and therefore can be grouped into two families, designated F and G. Family F enzymes show no sequence similarity with any known structure and their architecture is unknown. Studies of an inactive enzyme-substrate complex will help to elucidate the structural basis of binding and catalysis in the family F xylanases. RESULTS: We have therefore determined the crystal structure of the catalytic domain of a family F enzyme, Pseudomonas fluorescens subsp. cellulosa xylanase A, at 2.5 A resolution and a crystallographic R-factor of 0.20. The structure was solved using an engineered catalytic core in which the nucleophilic glutamate was replaced by a cysteine. As expected, this yielded both high-quality mercurial derivatives and an inactive enzyme which enabled the preparation of the inactive enzyme-substrate complex in the crystal. We show that family F xylanases are eight-fold alpha/beta-barrels (TIM barrels) with two active-site glutamates, one of which is the nucleophile and the other the acid-base. Xylopentaose binds to five subsites A-E with the cleaved bond between subsites D and E. Ca2+ binding, remote from the active-site glutamates, stabilizes the structure and may be involved in the binding of extended substrates. CONCLUSIONS: The architecture of P. fluorescens subsp. cellulosa has been determined crystallographically to be a commonly occurring enzyme fold, the eight-fold alpha/beta-barrel. Xylopentaose binds across the carboxy-terminal end of the alpha/beta-barrel in an active-site cleft which contains the two catalytic glutamates.

-	~~{{STRUCTURE_1xys\| PDB=1xys \| SCENE= }}~~	+	Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites.,Harris GW, Jenkins JA, Connerton I, Cummings N, Lo Leggio L, Scott M, Hazlewood GP, Laurie JI, Gilbert HJ, Pickersgill RW Structure. 1994 Nov 15;2(11):1107-16. PMID:7881909<ref>PMID:7881909</ref>

-	~~===CATALYTIC CORE OF XYLANASE A E246C MUTANT===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7881909}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xys]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:007881909<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Cellvibrio japonicus]]		[[Category: Cellvibrio japonicus]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]

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

OCA — Sat, 05 Jan 2013 13:50:22 GMT

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

←Older revision

Revision as of 13:50, 5 January 2013

OCA at 13:50, 5 January 2013

OCA — Sat, 05 Jan 2013 13:50:19 GMT

←Older revision		Revision as of 13:50, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xys.png\|left\|200px]]		[[Image:1xys.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xys", 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_1xys\| PDB=1xys \| SCENE= }}		{{STRUCTURE_1xys\| PDB=1xys \| SCENE= }}

	===CATALYTIC CORE OF XYLANASE A E246C MUTANT===		===CATALYTIC CORE OF XYLANASE A E246C MUTANT===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_7881909}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 7881909 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_7881909}}		{{ABSTRACT_PUBMED_7881909}}

	==About this Structure==		==About this Structure==
-	~~1XYS~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA].	+	[[1xys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~7881909~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007881909</ref><references group="xtra"/>
	[[Category: Cellvibrio japonicus]]		[[Category: Cellvibrio japonicus]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
Line 32:		Line 20:
	[[Category: Family 10 of glycosyl-hydrolase]]		[[Category: Family 10 of glycosyl-hydrolase]]
	[[Category: Family f xylanase]]		[[Category: Family f xylanase]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 09:45:53 2009''~~	+

OCA at 07:45, 17 February 2009

OCA — Tue, 17 Feb 2009 07:45:54 GMT

←Older revision		Revision as of 07:45, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1XYS is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA].	+	1XYS is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYS OCA].

	==Reference==		==Reference==
-	Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites., Harris GW, Jenkins JA, Connerton I, Cummings N, Lo Leggio L, Scott M, Hazlewood GP, Laurie JI, Gilbert HJ, Pickersgill RW, Structure. 1994 Nov 15;2(11):1107-16. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/7881909 7881909]~~	+	<ref group="xtra">PMID:7881909</ref><references group="xtra"/>
	[[Category: Cellvibrio japonicus]]		[[Category: Cellvibrio japonicus]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: Single protein]]
	[[Category: Connerton, I.]]		[[Category: Connerton, I.]]
	[[Category: Harris, G W.]]		[[Category: Harris, G W.]]
Line 34:		Line 33:
	[[Category: Family f xylanase]]		[[Category: Family f xylanase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 13~~:25:~~49 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:45:53 2009''