5yn3 - Revision history

OCA at 08:33, 22 November 2023

2023-11-22T08:33:14Z

←Older revision		Revision as of 08:33, 22 November 2023
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	<StructureSection load='5yn3' size='340' side='right'caption='[[5yn3]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5yn3' size='340' side='right'caption='[[5yn3]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yn3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pirse Pirse~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YN3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YN3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yn3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Piromyces_sp._E2 Piromyces sp. E2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YN3 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>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>xylA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~73868 PIRSE])</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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5]~~ </~~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=5yn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yn3 OCA], [https://pdbe.org/5yn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yn3 RCSB], [https://www.ebi.ac.uk/pdbsum/5yn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yn3 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=5yn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yn3 OCA], [~~http~~://pdbe.org/5yn3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yn3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yn3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yn3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9P8C9_PIRSE Q9P8C9_PIRSE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pirse]]~~	+	[[Category: Piromyces sp. E2]]
-	~~[[Category: Xylose isomerase~~]]	+	[[Category: Kim K-J]]
-	[[Category: Kim, K J]]	+	[[Category: Son H-F]]
-	[[Category: Son, H F]]	+
-	~~[[Category: Isomerase~~]]	+

OCA at 09:46, 9 September 2020

2020-09-09T09:46:36Z

←Older revision		Revision as of 09:46, 9 September 2020
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-	==Crystal ~~strcuture~~ of xylose isomerase from Piromyces sp. E2==	+	==Crystal structure of xylose isomerase from Piromyces sp. E2==
-	<StructureSection load='5yn3' size='340' side='right' caption='[[5yn3]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5yn3' size='340' side='right'caption='[[5yn3]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yn3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pirse Pirse]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YN3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YN3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yn3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pirse Pirse]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YN3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YN3 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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xylA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=73868 PIRSE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xylA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=73868 PIRSE])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=5yn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yn3 OCA], [http://pdbe.org/5yn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yn3 RCSB], [http://www.ebi.ac.uk/pdbsum/5yn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yn3 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=5yn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yn3 OCA], [http://pdbe.org/5yn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yn3 RCSB], [http://www.ebi.ac.uk/pdbsum/5yn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yn3 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: Large Structures]]
	[[Category: Pirse]]		[[Category: Pirse]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA at 05:55, 16 May 2018

2018-05-16T05:55:04Z

←Older revision		Revision as of 05:55, 16 May 2018
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	<StructureSection load='5yn3' size='340' side='right' caption='[[5yn3]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5yn3' size='340' side='right' caption='[[5yn3]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yn3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YN3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YN3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yn3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pirse Pirse]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YN3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YN3 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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xylA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=73868 PIRSE])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=5yn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yn3 OCA], [http://pdbe.org/5yn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yn3 RCSB], [http://www.ebi.ac.uk/pdbsum/5yn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yn3 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=5yn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yn3 OCA], [http://pdbe.org/5yn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yn3 RCSB], [http://www.ebi.ac.uk/pdbsum/5yn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yn3 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pirse]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Son, H F]]		[[Category: Son, H F]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 06:14, 9 May 2018

2018-05-09T06:14:01Z

←Older revision		Revision as of 06:14, 9 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yn3 is ~~ON HOLD until Paper~~ Publication	+	==Crystal strcuture of xylose isomerase from Piromyces sp. E2==
		+	<StructureSection load='5yn3' size='340' side='right' caption='[[5yn3]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yn3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YN3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YN3 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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=5yn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yn3 OCA], [http://pdbe.org/5yn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yn3 RCSB], [http://www.ebi.ac.uk/pdbsum/5yn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yn3 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biofuel production using lignocellulosic biomass is gaining attention because it can be substituted for fossil fuels without competing with edible resources. However, because Saccharomyces cerevisiae does not have a D-xylose metabolic pathway, oxidoreductase or isomerase pathways must be introduced to utilize D-xylose from lignocellulosic biomass in S. cerevisiae. To elucidate the biochemical properties of xylose isomerase (XI) from Piromyces sp. E2 (PsXI), we determine its crystal structure in complex with substrate mimic glycerol. An amino acid sequence comparison with other reported XIs and the relative activity measurements using five kinds of divalent metal ions confirmed that PsXI belongs to class II XI. Moreover kinetic analysis of PsXI was also performed using Mn(2)(+), the preferred divalent metal ion for PsXI. In addition, the substrate-binding mode of PsXI could be predicted with the substrate mimic glycerol bound to the active site. These studies may provide structural information to enhance D-xylose utilization for biofuel production.

-	~~Authors: Son, H~~.-F., ~~Kim~~, K.-J.	+	Crystal Structure and Biochemical Characterization of Xylose Isomerase from Piromyces sp. E2.,Son H, Lee SM, Kim KJ J Microbiol Biotechnol. 2018 Apr 28;28(4):571-578. doi: 10.4014/jmb.1711.11026. PMID:29385668<ref>PMID:29385668</ref>

-	~~Description: Crystal strcuture~~ of ~~xylose isomerase from Piromyces sp~~. E2	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Son, H.-F]]	+	<div class="pdbe-citations 5yn3" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kim, K.-J~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Xylose isomerase]]
		+	[[Category: Kim, K J]]
		+	[[Category: Son, H F]]
		+	[[Category: Isomerase]]

OCA at 06:31, 2 May 2018

2018-05-02T06:31:05Z

←Older revision		Revision as of 06:31, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yn3 is ON HOLD	+	The entry 5yn3 is ON HOLD until Paper Publication

	Authors: Son, H.-F., Kim, K.-J.		Authors: Son, H.-F., Kim, K.-J.

OCA at 04:37, 31 January 2018

2018-01-31T04:37:02Z

←Older revision		Revision as of 04:37, 31 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yn3 is ON HOLD ~~until Paper Publication~~	+	The entry 5yn3 is ON HOLD

	Authors: Son, H.-F., Kim, K.-J.		Authors: Son, H.-F., Kim, K.-J.
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	Description: Crystal strcuture of xylose isomerase from Piromyces sp. E2		Description: Crystal strcuture of xylose isomerase from Piromyces sp. E2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kim, K.-J]]
	[[Category: Son, H.-F]]		[[Category: Son, H.-F]]
		+	[[Category: Kim, K.-J]]

OCA at 04:54, 29 November 2017

2017-11-29T04:54:41Z

←Older revision		Revision as of 04:54, 29 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yn3 is ON HOLD	+	The entry 5yn3 is ON HOLD until Paper Publication

	Authors: Son, H.-F., Kim, K.-J.		Authors: Son, H.-F., Kim, K.-J.

OCA: Protected "5yn3" [edit=sysop:move=sysop]

2017-11-01T04:46:40Z

Protected "5yn3" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:46, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yn3 is ON HOLD Authors: Son, H.-F., Kim, K.-J. Description: Crystal strcuture of xylose isomerase from Piromyces sp. E2 [[Category: Unreleased Str...

2017-11-01T04:46:39Z

New page: '''Unreleased structure''' The entry 5yn3 is ON HOLD Authors: Son, H.-F., Kim, K.-J. Description: Crystal strcuture of xylose isomerase from Piromyces sp. E2 [[Category: Unreleased Str...

New page

'''Unreleased structure'''

The entry 5yn3 is ON HOLD

Authors: Son, H.-F., Kim, K.-J.

Description: Crystal strcuture of xylose isomerase from Piromyces sp. E2
[[Category: Unreleased Structures]]
[[Category: Kim, K.-J]]
[[Category: Son, H.-F]]