5k6m - Revision history

OCA at 10:41, 27 September 2023

OCA — Wed, 27 Sep 2023 10:41:57 GMT

←Older revision		Revision as of 10:41, 27 September 2023
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	==Structure of a GH3 b-glIcosidase from cow rumen metagenome in complex with glucose==		==Structure of a GH3 b-glIcosidase from cow rumen metagenome in complex with glucose==
-	<StructureSection load='5k6m' size='340' side='right' caption='[[5k6m]], [[Resolution\|resolution]] 2.17Å' scene=''>	+	<StructureSection load='5k6m' size='340' side='right'caption='[[5k6m]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k6m]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Environmental_sequence Environmental sequence~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K6M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k6m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Metagenome Metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K6M FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.17Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5k6l\|5k6l~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>glyA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~256318 environmental sequence])</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=5k6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6m OCA], [https://pdbe.org/5k6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k6m RCSB], [https://www.ebi.ac.uk/pdbsum/5k6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6m 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/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21]~~ </~~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=5k6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6m OCA], [~~http~~://pdbe.org/5k6m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k6m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k6m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6m ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-glucosidase]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Environmental sequence]]~~	+
-	~~[[Category: Ramirez-Escudero, M]]~~	+
-	~~[[Category: Sanz-Aparicio, J]]~~	+
-	~~[[Category: B-glicosidase]]~~	+
-	~~[[Category: Functional food]]~~	+
-	~~[[Category: Glucose]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+
	[[Category: Metagenome]]		[[Category: Metagenome]]
-	[[Category: ~~Microbiota~~]]	+	[[Category: Ramirez-Escudero M]]
-	[[Category: ~~Prebiotic~~]]	+	[[Category: Sanz-Aparicio J]]

OCA at 06:07, 8 March 2018

OCA — Thu, 08 Mar 2018 06:07:39 GMT

←Older revision		Revision as of 06:07, 8 March 2018
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	<StructureSection load='5k6m' size='340' side='right' caption='[[5k6m]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5k6m' size='340' side='right' caption='[[5k6m]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k6m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k6m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Environmental_sequence Environmental sequence]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K6M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k6l\|5k6l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k6l\|5k6l]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glyA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=256318 environmental sequence])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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=5k6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6m OCA], [http://pdbe.org/5k6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6m RCSB], [http://www.ebi.ac.uk/pdbsum/5k6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6m ProSAT]</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=5k6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6m OCA], [http://pdbe.org/5k6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6m RCSB], [http://www.ebi.ac.uk/pdbsum/5k6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6m ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Beta-glucosidase]]		[[Category: Beta-glucosidase]]
		+	[[Category: Environmental sequence]]
	[[Category: Ramirez-Escudero, M]]		[[Category: Ramirez-Escudero, M]]
	[[Category: Sanz-Aparicio, J]]		[[Category: Sanz-Aparicio, J]]

OCA at 09:51, 19 October 2016

OCA — Wed, 19 Oct 2016 09:51:29 GMT

←Older revision		Revision as of 09:51, 19 October 2016
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	<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=5k6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6m OCA], [http://pdbe.org/5k6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6m RCSB], [http://www.ebi.ac.uk/pdbsum/5k6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6m ProSAT]</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=5k6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6m OCA], [http://pdbe.org/5k6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6m RCSB], [http://www.ebi.ac.uk/pdbsum/5k6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6m ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Metagenomics has opened up a vast pool of genes for putative, yet uncharacterized, enzymes. It widens our knowledge on the enzyme diversity world and discloses new families for which a clear classification is still needed, as it exemplified by glycosyl hydrolase (GH) family-3 proteins. Herein, we describe a GH3 enzyme (GlyA1) from resident microbial communities in strained ruminal fluid. The enzyme is a beta-glucosidase/beta-xylosidase that also shows beta-galactosidase, beta-fucosidase, alpha-arabinofuranosidase and alpha-arabinopyranosidase activities. Short cello- and xylo-oligosaccharides, sophorose and gentibiose are among the preferred substrates, the large polysaccharide lichenan being also hydrolysed by GlyA1. The determination of the crystal structure of the enzyme in combination with deletion and site-directed mutagenesis allowed identifying its unusual domain composition and the active site architecture. Complexes of GlyA1 with glucose, galactose and xylose allowed picturing the catalytic pocket and illustrated the molecular basis of the broad substrate specificity. A hydrophobic platform defined by residues Trp711 and Trp106, located in a highly mobile loop, appears able to allocate differently beta-linked bioses. GlyA1 includes an additional C-terminal domain previously unobserved in GH3 members, but crystallization of the full-length enzyme was unsuccessful. Therefore, small angle x-ray experiments have been performed to investigate the molecular flexibility and overall putative shape. This study provided evidences that GlyA1 defines a new subfamily of GH3 proteins with a novel permuted domain topology. Phylogenetic analysis indicates that this topology is associated with microbes inhabiting the digestive tracts of ruminants and other animals, feeding on chemically diverse plant polymeric materials.
		+
		+	Structural and functional characterization of a ruminal beta-glycosidase defines a novel subfamily of glycosyl hydrolase family 3 with permuted domain topology.,Ramirez-Escudero M, Del Pozo MV, Marin-Navarro J, Gonzalez B, Golyshin PN, Polaina J, Ferrer M, Sanz-Aparicio J J Biol Chem. 2016 Sep 27. pii: jbc.M116.747527. PMID:27679487<ref>PMID:27679487</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5k6m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:31, 5 October 2016

OCA — Wed, 05 Oct 2016 21:31:59 GMT

←Older revision		Revision as of 21:31, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k6m is ~~ON HOLD until Paper Publication~~	+	==Structure of a GH3 b-glIcosidase from cow rumen metagenome in complex with glucose==
-		+	<StructureSection load='5k6m' size='340' side='right' caption='[[5k6m]], [[Resolution\|resolution]] 2.17Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5k6m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K6M FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k6l\|5k6l]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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=5k6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6m OCA], [http://pdbe.org/5k6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6m RCSB], [http://www.ebi.ac.uk/pdbsum/5k6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6m ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-glucosidase]]
		+	[[Category: Ramirez-Escudero, M]]
		+	[[Category: Sanz-Aparicio, J]]
		+	[[Category: B-glicosidase]]
		+	[[Category: Functional food]]
		+	[[Category: Glucose]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metagenome]]
		+	[[Category: Microbiota]]
		+	[[Category: Prebiotic]]

OCA at 13:29, 20 June 2016

OCA — Mon, 20 Jun 2016 13:29:03 GMT

←Older revision		Revision as of 13:29, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k6m is ON HOLD	+	The entry 5k6m is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5k6m" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:23:42 GMT

Protected "5k6m" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:23, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k6m is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:23:41 GMT

New page: '''Unreleased structure''' The entry 5k6m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k6m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]