5glm - Revision history

OCA at 11:35, 2 August 2023

2023-08-02T11:35:26Z

←Older revision		Revision as of 11:35, 2 August 2023
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	==Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome in complex with xylotriose, calcium-free form.==		==Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome in complex with xylotriose, calcium-free form.==
-	<StructureSection load='5glm' size='340' side='right' caption='[[5glm]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5glm' size='340' side='right'caption='[[5glm]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5glm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Uncultivated_bacterium Uncultivated~~ bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5glm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GLM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5glk\|5glk]], [[5gll\|5gll]], [[5gln\|5gln]], [[5glo\|5glo]], [[5glp\|5glp]], [[5glq\|5glq]], [[5glr\|5glr]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=PRD_900117:4beta-beta-xylotriose'>PRD_900117</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">coxyl43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=77133 uncultivated bacterium])</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=5glm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glm OCA], [https://pdbe.org/5glm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5glm RCSB], [https://www.ebi.ac.uk/pdbsum/5glm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5glm 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=5glm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glm OCA], [~~http~~://pdbe.org/5glm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5glm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5glm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5glm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H5BL38_9BACT A0A0H5BL38_9BACT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Uncultivated~~ bacterium]]	+	[[Category: Large Structures]]
-	[[Category: Fujimoto, Z]]	+	[[Category: Uncultured bacterium]]
-	[[Category: Kishine, N]]	+	[[Category: Fujimoto Z]]
-	[[Category: Matsuzawa, T]]	+	[[Category: Kishine N]]
-	[[Category: Yaoi, K]]	+	[[Category: Matsuzawa T]]
-	~~[[Category: Glycoside hydrolase family 43]]~~	+	[[Category: Yaoi K]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:32, 6 December 2017

2017-12-06T07:32:55Z

←Older revision		Revision as of 07:32, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5glm' size='340' side='right' caption='[[5glm]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5glm' size='340' side='right' caption='[[5glm]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5glm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5glm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GLM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5glk\|5glk]], [[5gll\|5gll]], [[5gln\|5gln]], [[5glo\|5glo]], [[5glp\|5glp]], [[5glq\|5glq]], [[5glr\|5glr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5glk\|5glk]], [[5gll\|5gll]], [[5gln\|5gln]], [[5glo\|5glo]], [[5glp\|5glp]], [[5glq\|5glq]], [[5glr\|5glr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">coxyl43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=77133 uncultivated bacterium])</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=5glm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glm OCA], [http://pdbe.org/5glm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5glm RCSB], [http://www.ebi.ac.uk/pdbsum/5glm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5glm 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=5glm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glm OCA], [http://pdbe.org/5glm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5glm RCSB], [http://www.ebi.ac.uk/pdbsum/5glm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5glm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of metagenomic beta-xylosidase/alpha-l-arabinofuranosidase CoXyl43, activated by calcium ions, was determined in its apo and complexed forms with xylotriose or l-arabinose in the presence and absence of calcium. The presence of calcium ions dramatically increases the kcat of CoXyl43 for p-nitrophenyl beta-d-xylopyranoside and reduces the Michaelis constant for p-nitrophenyl alpha-l-arabinofuranoside. CoXyl43 consists of a single catalytic domain comprised of a five-bladed beta-propeller. In the presence of calcium, a single calcium ion was observed at the centre of this catalytic domain, behind the catalytic pocket. In the absence of calcium, the calcium ion was replaced with one sodium ion and one water molecule, and the positions of these cations were shifted by 1.3 A. The histidine-319 side chain, which coordinates to the 2-hydroxyl oxygen atom of the bound xylose molecule in the catalytic pocket, also coordinates to the calcium ion, but not to the sodium ion. The calcium-dependent increase in activity appears to be caused by the structural change in the catalytic pocket induced by the tightly bound calcium ion and coordinating water molecules, and by the protonation state of glutamic acid-268, the catalytic acid of the enzyme. Our findings further elucidate the complex relationship between metal ions and glycosidases.
		+
		+	Crystal structure of metagenomic beta-xylosidase/ alpha-l-arabinofuranosidase activated by calcium.,Matsuzawa T, Kaneko S, Kishine N, Fujimoto Z, Yaoi K J Biochem. 2017 Sep 1;162(3):173-181. doi: 10.1093/jb/mvx012. PMID:28204531<ref>PMID:28204531</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5glm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Uncultivated bacterium]]
	[[Category: Fujimoto, Z]]		[[Category: Fujimoto, Z]]
	[[Category: Kishine, N]]		[[Category: Kishine, N]]

OCA at 21:10, 15 March 2017

2017-03-15T21:10:07Z

←Older revision		Revision as of 21:10, 15 March 2017
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-	'''Unreleased structure'''

-	~~The entry 5glm is ON HOLD until Paper Publication~~	+	==Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome in complex with xylotriose, calcium-free form.==
-		+	<StructureSection load='5glm' size='340' side='right' caption='[[5glm]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors: Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5glm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GLM FirstGlance]. <br>
-	~~Description:~~ Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome in complex with xylotriose, calcium-free form.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5glk\|5glk]], [[5gll\|5gll]], [[5gln\|5gln]], [[5glo\|5glo]], [[5glp\|5glp]], [[5glq\|5glq]], [[5glr\|5glr]]</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=5glm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glm OCA], [http://pdbe.org/5glm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5glm RCSB], [http://www.ebi.ac.uk/pdbsum/5glm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5glm ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fujimoto, Z]]
		+	[[Category: Kishine, N]]
	[[Category: Matsuzawa, T]]		[[Category: Matsuzawa, T]]
	[[Category: Yaoi, K]]		[[Category: Yaoi, K]]
-	[[Category: ~~Kishine, N~~]]	+	[[Category: Glycoside hydrolase family 43]]
-	[[Category: ~~Fujimoto, Z~~]]	+	[[Category: Hydrolase]]

OCA at 08:58, 9 March 2017

2017-03-09T08:58:45Z

←Older revision		Revision as of 08:58, 9 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Matsuzawa, T]]		[[Category: Matsuzawa, T]]
		+	[[Category: Yaoi, K]]
	[[Category: Kishine, N]]		[[Category: Kishine, N]]
	[[Category: Fujimoto, Z]]		[[Category: Fujimoto, Z]]
-	[[Category: Yaoi, K]]

OCA at 17:10, 25 January 2017

2017-01-25T17:10:39Z

←Older revision		Revision as of 17:10, 25 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K.		Authors: Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K.

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

2016-07-26T09:44:22Z

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

←Older revision

Revision as of 09:44, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5glm is ON HOLD Authors: Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K. Description: Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-a...

2016-07-26T09:44:21Z

New page: '''Unreleased structure''' The entry 5glm is ON HOLD Authors: Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K. Description: Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-a...

New page

'''Unreleased structure'''

The entry 5glm is ON HOLD

Authors: Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K.

Description: Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome in complex with xylotriose, calcium-free form.
[[Category: Unreleased Structures]]
[[Category: Matsuzawa, T]]
[[Category: Kishine, N]]
[[Category: Fujimoto, Z]]
[[Category: Yaoi, K]]