5z6t - Revision history

OCA at 08:46, 22 November 2023

OCA — Wed, 22 Nov 2023 08:46:59 GMT

←Older revision		Revision as of 08:46, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5z6t' size='340' side='right'caption='[[5z6t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5z6t' size='340' side='right'caption='[[5z6t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Picst Picst~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Z6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Scheffersomyces_stipitis_CBS_6054 Scheffersomyces stipitis CBS 6054]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z6T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>XYL1, PICST_89614 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=322104 PICST])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/D~~-~~xylose_reductase D~~-~~xylose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.307 1.1.1.307]~~ </~~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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [https://pdbe.org/5z6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [https://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t 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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [~~http~~://pdbe.org/5z6t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/XYL1_PICST XYL1_PICST]] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.<ref>PMID:3921014</ref>	+	[https://www.uniprot.org/uniprot/XYL1_PICST XYL1_PICST] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.<ref>PMID:3921014</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: D-xylose reductase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Picst~~]]	+	[[Category: Scheffersomyces stipitis CBS 6054]]
-	[[Category: Kim~~, K J~~]]	+	[[Category: Kim KJ]]
-	[[Category: Son~~, H F]]~~	+	[[Category: Son HF]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pentose metabolism]]~~	+
-	~~[[Category: Scheffersomyces stipitis]]~~	+
-	~~[[Category: Xylose reductase~~]]	+

OCA at 09:46, 9 September 2020

OCA — Wed, 09 Sep 2020 09:46:36 GMT

←Older revision		Revision as of 09:46, 9 September 2020
Line 1:		Line 1:

-	==Crystal ~~strcuture~~ of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH==	+	==Crystal structure of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH==
-	<StructureSection load='5z6t' size='340' side='right' caption='[[5z6t]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5z6t' size='340' side='right'caption='[[5z6t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Picst Picst]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Picst Picst]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z6T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XYL1, PICST_89614 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=322104 PICST])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XYL1, PICST_89614 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=322104 PICST])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-xylose_reductase D-xylose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.307 1.1.1.307] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-xylose_reductase D-xylose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.307 1.1.1.307] </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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [http://pdbe.org/5z6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [http://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t 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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [http://pdbe.org/5z6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [http://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: D-xylose reductase]]		[[Category: D-xylose reductase]]
		+	[[Category: Large Structures]]
	[[Category: Picst]]		[[Category: Picst]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]

OCA at 08:46, 19 December 2018

OCA — Wed, 19 Dec 2018 08:46:50 GMT

←Older revision		Revision as of 08:46, 19 December 2018
Line 3:		Line 3:
	<StructureSection load='5z6t' size='340' side='right' caption='[[5z6t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5z6t' size='340' side='right' caption='[[5z6t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Picst Picst]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z6T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XYL1, PICST_89614 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=322104 PICST])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-xylose_reductase D-xylose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.307 1.1.1.307] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-xylose_reductase D-xylose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.307 1.1.1.307] </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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [http://pdbe.org/5z6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [http://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t 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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [http://pdbe.org/5z6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [http://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/XYL1_PICST XYL1_PICST]] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.<ref>PMID:3921014</ref>		[[http://www.uniprot.org/uniprot/XYL1_PICST XYL1_PICST]] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.<ref>PMID:3921014</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lignocellulosic biomass, of which D-xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D-xylose utilization, we determined the crystal structure of D-xylose reductase from Schefferzomyces stipitis (SsXR) at a 1.95 A resolution. We also determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. Phylogenetic tree analysis showed that AKR enzymes annotated with bacterial/archaeal XRs belonged to uncharacterized AKR families and might have no XR function, and yeast/fungi derived enzymes, which belong to the same group with SsXR, can be candidates for XR to increase xylose consumption.
		+
		+	Structural insight into D-xylose utilization by xylose reductase from Scheffersomyces stipitis.,Son HF, Lee SM, Kim KJ Sci Rep. 2018 Nov 28;8(1):17442. doi: 10.1038/s41598-018-35703-x. PMID:30487522<ref>PMID:30487522</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5z6t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 15:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: D-xylose reductase]]		[[Category: D-xylose reductase]]
		+	[[Category: Picst]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Son, H F]]		[[Category: Son, H F]]

OCA at 06:30, 5 December 2018

OCA — Wed, 05 Dec 2018 06:30:25 GMT

←Older revision		Revision as of 06:30, 5 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z6t is ~~ON HOLD until Paper Publication~~	+	==Crystal strcuture of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH==
-		+	<StructureSection load='5z6t' size='340' side='right' caption='[[5z6t]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Son~~, H.F., ~~Kim~~, K.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z6T FirstGlance]. <br>
-	~~Description~~: ~~Crystal strcuture of~~ D-xylose ~~reductase from Scheffersomyces stipitis in complex with~~ NADPH	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-xylose_reductase D-xylose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.307 1.1.1.307] </span></td></tr>
-	[[Category: Son, H.F]]	+	<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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [http://pdbe.org/5z6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [http://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t ProSAT]</span></td></tr>
-	[[Category: ~~Kim, K.J~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/XYL1_PICST XYL1_PICST]] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.<ref>PMID:3921014</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: D-xylose reductase]]
		+	[[Category: Kim, K J]]
		+	[[Category: Son, H F]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pentose metabolism]]
		+	[[Category: Scheffersomyces stipitis]]
		+	[[Category: Xylose reductase]]

OCA at 04:59, 7 February 2018

OCA — Wed, 07 Feb 2018 04:59:17 GMT

←Older revision		Revision as of 04:59, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z6t is ON HOLD	+	The entry 5z6t is ON HOLD until Paper Publication

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

	Description: Crystal strcuture of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH		Description: Crystal strcuture of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Son, H.-F]]	+	[[Category: Son, H.F]]
-	[[Category: Kim, K.-J]]	+	[[Category: Kim, K.J]]

OCA: Protected "5z6t" [edit=sysop:move=sysop]

OCA — Wed, 31 Jan 2018 04:42:14 GMT

Protected "5z6t" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:42, 31 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z6t is ON HOLD Authors: Son, H.-F., Kim, K.-J. Description: Crystal strcuture of D-xylose reductase from Scheffersomyces stipitis in complex with ...

OCA — Wed, 31 Jan 2018 04:42:13 GMT

New page: '''Unreleased structure''' The entry 5z6t is ON HOLD Authors: Son, H.-F., Kim, K.-J. Description: Crystal strcuture of D-xylose reductase from Scheffersomyces stipitis in complex with ...

New page

'''Unreleased structure'''

The entry 5z6t is ON HOLD

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

Description: Crystal strcuture of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH
[[Category: Unreleased Structures]]
[[Category: Son, H.-F]]
[[Category: Kim, K.-J]]