1pz3 - Revision history

OCA at 08:11, 14 February 2024

OCA — Wed, 14 Feb 2024 08:11:33 GMT

←Older revision		Revision as of 08:11, 14 February 2024
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	<StructureSection load='1pz3' size='340' side='right'caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='1pz3' size='340' side='right'caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.75Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1pz2\|1pz2]]~~, [[~~1qw8~~\|~~1qw8]], [[1qw9\|1qw9~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1422 ATCC 12980])</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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [https://pdbe.org/1pz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [https://www.ebi.ac.uk/pdbsum/1pz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz3 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </~~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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [~~http~~://pdbe.org/1pz3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pz3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/IABF_GEOSE IABF_GEOSE]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref> <ref>PMID:7887599</ref>	+	[https://www.uniprot.org/uniprot/IABF_GEOSE IABF_GEOSE] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref> <ref>PMID:7887599</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pz3 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=1pz3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.
-
-	Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.,Hovel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D EMBO J. 2003 Oct 1;22(19):4922-32. PMID:14517232<ref>PMID:14517232</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pz3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Non-reducing end alpha-L-arabinofuranosidase]]~~	+	[[Category: Baasov T]]
-	[[Category: Baasov, T]]	+	[[Category: Belakhov V]]
-	[[Category: Belakhov, V]]	+	[[Category: Hoevel K]]
-	[[Category: Hoevel, K]]	+	[[Category: Niefind K]]
-	[[Category: Niefind, K]]	+	[[Category: Schomburg D]]
-	[[Category: Schomburg, D]]	+	[[Category: Shallom D]]
-	[[Category: Shallom, D]]	+	[[Category: Shoham G]]
-	[[Category: Shoham, G]]	+	[[Category: Shoham Y]]
-	[[Category: Shoham, Y]]	+
-	~~[[Category: Beta-alpha8-barrel]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:39, 9 December 2020

OCA — Wed, 09 Dec 2020 07:39:08 GMT

←Older revision		Revision as of 07:39, 9 December 2020
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	==Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6==		==Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6==
-	<StructureSection load='1pz3' size='340' side='right' caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='1pz3' size='340' side='right'caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pz2\|1pz2]], [[1qw8\|1qw8]], [[1qw9\|1qw9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1pz2\|1pz2]], [[1qw8\|1qw8]], [[1qw9\|1qw9]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://pdbe.org/1pz3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz3 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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://pdbe.org/1pz3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pz/1pz3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pz/1pz3_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 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
		+	[[Category: Large Structures]]
	[[Category: Non-reducing end alpha-L-arabinofuranosidase]]		[[Category: Non-reducing end alpha-L-arabinofuranosidase]]
	[[Category: Baasov, T]]		[[Category: Baasov, T]]

OCA at 08:55, 12 October 2017

OCA — Thu, 12 Oct 2017 08:55:17 GMT

←Older revision		Revision as of 08:55, 12 October 2017
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		+
	==Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6==		==Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6==
	<StructureSection load='1pz3' size='340' side='right' caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='1pz3' size='340' side='right' caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://pdbe.org/1pz3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://pdbe.org/1pz3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 02:42, 8 February 2016

OCA — Mon, 08 Feb 2016 02:42:58 GMT

←Older revision		Revision as of 02:42, 8 February 2016
Line 19:		Line 19:
	<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=1pz3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:06, 10 September 2015

OCA — Thu, 10 Sep 2015 07:06:38 GMT

←Older revision		Revision as of 07:06, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1pz3' size='340' side='right' caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='1pz3' size='340' side='right' caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pz2\|1pz2]], [[1qw8\|1qw8]], [[1qw9\|1qw9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pz2\|1pz2]], [[1qw8\|1qw8]], [[1qw9\|1qw9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ~~Geobacillus stearothermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Alpha~~-N-arabinofuranosidase ~~Alpha~~-N-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://pdbe.org/1pz3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~ABFA_BACST ABFA_BACST~~]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:~~7887599~~</ref> <ref>PMID:~~11943144~~</ref> <ref>PMID:~~12221104~~</ref> <ref>PMID:~~14517232~~</ref>	+	[[http://www.uniprot.org/uniprot/IABF_GEOSE IABF_GEOSE]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref> <ref>PMID:7887599</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	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 1pz3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alpha-N-arabinofuranosidase~~]]	+	[[Category: Atcc 12980]]
-	[[Category: ~~Geobacillus stearothermophilus~~]]	+	[[Category: Non-reducing end alpha-L-arabinofuranosidase]]
	[[Category: Baasov, T]]		[[Category: Baasov, T]]
	[[Category: Belakhov, V]]		[[Category: Belakhov, V]]

OCA at 19:59, 24 December 2014

OCA — Wed, 24 Dec 2014 19:59:34 GMT

←Older revision		Revision as of 19:59, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pz2\|1pz2]], [[1qw8\|1qw8]], [[1qw9\|1qw9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pz2\|1pz2]], [[1qw8\|1qw8]], [[1qw9\|1qw9]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-N-arabinofuranosidase Alpha-N-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-N-arabinofuranosidase Alpha-N-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ABFA_BACST ABFA_BACST]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:7887599</ref> <ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Alpha-N-arabinofuranosidase]]		[[Category: Alpha-N-arabinofuranosidase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Baasov, T.]]	+	[[Category: Baasov, T]]
-	[[Category: Belakhov, V.]]	+	[[Category: Belakhov, V]]
-	[[Category: Hoevel, K.]]	+	[[Category: Hoevel, K]]
-	[[Category: Niefind, K.]]	+	[[Category: Niefind, K]]
-	[[Category: Schomburg, D.]]	+	[[Category: Schomburg, D]]
-	[[Category: Shallom, D.]]	+	[[Category: Shallom, D]]
-	[[Category: Shoham, G.]]	+	[[Category: Shoham, G]]
-	[[Category: Shoham, Y.]]	+	[[Category: Shoham, Y]]
	[[Category: Beta-alpha8-barrel]]		[[Category: Beta-alpha8-barrel]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 16:02, 29 September 2014

OCA — Mon, 29 Sep 2014 16:02:02 GMT

←Older revision		Revision as of 16:02, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1pz3.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6==
		+	<StructureSection load='1pz3' size='340' side='right' caption='[[1pz3]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pz3]] is a 2 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=1PZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PZ3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pz2\|1pz2]], [[1qw8\|1qw8]], [[1qw9\|1qw9]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-N-arabinofuranosidase Alpha-N-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=1pz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pz3 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/pz/1pz3_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 ==
		+	High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.

-	~~{{STRUCTURE_1pz3\| PDB=1pz3 \| SCENE= }}~~	+	Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.,Hovel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D EMBO J. 2003 Oct 1;22(19):4922-32. PMID:14517232<ref>PMID:14517232</ref>

-	~~===Crystal structure~~ of ~~a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14517232}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1pz3]] is a 2 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=1PZ3 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:014517232<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alpha-N-arabinofuranosidase]]		[[Category: Alpha-N-arabinofuranosidase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]

OCA: Protected "1pz3" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 10:12:43 GMT

Protected "1pz3" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:12, 2 January 2013

OCA at 10:12, 2 January 2013

OCA — Wed, 02 Jan 2013 10:12:40 GMT

←Older revision		Revision as of 10:12, 2 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pz3.png\|left\|200px]]		[[Image:1pz3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pz3", 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_1pz3\| PDB=1pz3 \| SCENE= }}		{{STRUCTURE_1pz3\| PDB=1pz3 \| SCENE= }}

	===Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6===		===Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14517232}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14517232 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14517232}}		{{ABSTRACT_PUBMED_14517232}}

	==About this Structure==		==About this Structure==
-	~~1PZ3~~ is a 2 ~~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=1PZ3 OCA].	+	[[1pz3]] is a 2 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=1PZ3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14517232~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014517232</ref><references group="xtra"/>
	[[Category: Alpha-N-arabinofuranosidase]]		[[Category: Alpha-N-arabinofuranosidase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
Line 35:		Line 23:
	[[Category: Shoham, Y.]]		[[Category: Shoham, Y.]]
	[[Category: Beta-alpha8-barrel]]		[[Category: Beta-alpha8-barrel]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 18:13:38 2009''~~	+

OCA at 16:13, 16 February 2009

OCA — Mon, 16 Feb 2009 16:13:39 GMT

←Older revision		Revision as of 16:13, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1PZ3 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=1PZ3 OCA].	+	1PZ3 is a 2 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=1PZ3 OCA].

	==Reference==		==Reference==
-	Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase., Hovel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D, EMBO J. 2003 Oct 1;22(19):4922-32. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/14517232 14517232]~~	+	<ref group="xtra">PMID:14517232</ref><references group="xtra"/>
	[[Category: Alpha-N-arabinofuranosidase]]		[[Category: Alpha-N-arabinofuranosidase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Single protein]]
	[[Category: Baasov, T.]]		[[Category: Baasov, T.]]
	[[Category: Belakhov, V.]]		[[Category: Belakhov, V.]]
Line 37:		Line 36:
	[[Category: Beta-alpha8-barrel]]		[[Category: Beta-alpha8-barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 21~~:52:~~04 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:13:38 2009''