5xqk - Revision history

OCA at 08:10, 22 November 2023

OCA — Wed, 22 Nov 2023 08:10:20 GMT

←Older revision		Revision as of 08:10, 22 November 2023
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	==Crystal Structure of Transketolase in complex with xylulose-5-phosphate from Pichia Stipitis==		==Crystal Structure of Transketolase in complex with xylulose-5-phosphate from Pichia Stipitis==
-	<StructureSection load='5xqk' size='340' side='right' caption='[[5xqk]], [[Resolution\|resolution]] 1.12Å' scene=''>	+	<StructureSection load='5xqk' size='340' side='right'caption='[[5xqk]], [[Resolution\|resolution]] 1.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xqk]] is a 1 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=5XQK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xqk]] is a 1 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=5XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XQK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=T5X:2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-2-YL}-5-O-PHOSPHONO-D-XYLITOL'>T5X</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]] 1.12Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TKT, TKT1, PICST_67105 ([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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=T5X:2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-2-YL}-5-O-PHOSPHONO-D-XYLITOL'>T5X</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transketolase Transketolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.1 2.2.1.1] </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=5xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqk OCA], [https://pdbe.org/5xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xqk RCSB], [https://www.ebi.ac.uk/pdbsum/5xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqk 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=5xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqk OCA], [~~http~~://pdbe.org/5xqk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xqk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xqk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TKT_PICST TKT_PICST]] Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.	+	[https://www.uniprot.org/uniprot/TKT_PICST TKT_PICST] Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:

	==See Also==		==See Also==
-	*[[Transketolase\|Transketolase]]	+	*[[Transketolase 3D structures\|Transketolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Picst~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Transketolase~~]]	+	[[Category: Scheffersomyces stipitis CBS 6054]]
-	[[Category: Hsu~~, N S~~]]	+	[[Category: Hsu NS]]
-	[[Category: Li~~, T L~~]]	+	[[Category: Li TL]]
-	[[Category: Wang~~, Y L]]~~	+	[[Category: Wang YL]]
-	~~[[Category: Transferase~~]]	+

OCA at 08:44, 19 December 2018

OCA — Wed, 19 Dec 2018 08:44:55 GMT

←Older revision		Revision as of 08:44, 19 December 2018
Line 3:		Line 3:
	<StructureSection load='5xqk' size='340' side='right' caption='[[5xqk]], [[Resolution\|resolution]] 1.12Å' scene=''>		<StructureSection load='5xqk' size='340' side='right' caption='[[5xqk]], [[Resolution\|resolution]] 1.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xqk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xqk]] is a 1 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=5XQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=T5X:2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-2-YL}-5-O-PHOSPHONO-D-XYLITOL'>T5X</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=T5X:2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-2-YL}-5-O-PHOSPHONO-D-XYLITOL'>T5X</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TKT, TKT1, PICST_67105 ([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/Transketolase Transketolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.1 2.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transketolase Transketolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.1 2.2.1.1] </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=5xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqk OCA], [http://pdbe.org/5xqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqk RCSB], [http://www.ebi.ac.uk/pdbsum/5xqk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqk 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=5xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqk OCA], [http://pdbe.org/5xqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqk RCSB], [http://www.ebi.ac.uk/pdbsum/5xqk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqk ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TKT_PICST TKT_PICST]] Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.		[[http://www.uniprot.org/uniprot/TKT_PICST TKT_PICST]] Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transketolase (TK) catalyzes a reversible transfer of a two-carbon (C2 ) unit between phosphoketose donors and phosphoaldose acceptors, for which the group-transfer reaction that follows a one- or two-electron mechanism and the force that breaks the C2"-C3" bond of the ketose donors remain unresolved. Herein, we report ultrahigh-resolution crystal structures of a TK (TKps) from Pichia stipitis in previously undiscovered intermediate states and support a diradical mechanism for a reversible group-transfer reaction. In conjunction with MS, NMR spectroscopy, EPR and computational analyses, it is concluded that the enzyme-catalyzed non-Kekule diradical cofactor brings about the C2"-C3" bond cleavage/formation for the C2 -unit transfer reaction, for which suppression of activation energy and activation and destabilization of enzymatic intermediates are facilitated.
		+
		+	Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions.,Hsu NS, Wang YL, Lin KH, Chang CF, Ke SC, Lyu SY, Hsu LJ, Li YS, Chen SC, Wang KC, Li TL Chembiochem. 2018 Nov 16;19(22):2395-2402. doi: 10.1002/cbic.201800378. Epub 2018, Oct 18. PMID:30155962<ref>PMID:30155962</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xqk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transketolase\|Transketolase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Picst]]
	[[Category: Transketolase]]		[[Category: Transketolase]]
	[[Category: Hsu, N S]]		[[Category: Hsu, N S]]

OCA at 07:34, 14 June 2018

OCA — Thu, 14 Jun 2018 07:34:36 GMT

←Older revision		Revision as of 07:34, 14 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xqk is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of Transketolase in complex with xylulose-5-phosphate from Pichia Stipitis==
-		+	<StructureSection load='5xqk' size='340' side='right' caption='[[5xqk]], [[Resolution\|resolution]] 1.12Å' scene=''>
-	~~Authors~~: Li, T.L., ~~Hsu~~, N.S., ~~Wang~~, Y.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xqk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQK FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure~~ of ~~Transketolase in complex with xylulose~~-~~5-phosphate~~ from ~~Pichia Stipitis~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=T5X:2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-2-YL}-5-O-PHOSPHONO-D-XYLITOL'>T5X</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/Transketolase Transketolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.1 2.2.1.1] </span></td></tr>
-	[[Category: Li, ~~T.L~~]]	+	<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=5xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqk OCA], [http://pdbe.org/5xqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqk RCSB], [http://www.ebi.ac.uk/pdbsum/5xqk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqk ProSAT]</span></td></tr>
-	[[Category: ~~Hsu~~, ~~N.S~~]]	+	</table>
-	[[Category: Wang, Y.L]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TKT_PICST TKT_PICST]] Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Transketolase]]
		+	[[Category: Hsu, N S]]
		+	[[Category: Li, T L]]
		+	[[Category: Wang, Y L]]
		+	[[Category: Transferase]]

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

OCA — Wed, 27 Sep 2017 15:41:08 GMT

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

←Older revision

Revision as of 15:41, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xqk is ON HOLD until Paper Publication Authors: Li, T.L., Hsu, N.S., Wang, Y.L. Description: Crystal Structure of Transketolase in complex with xy...

OCA — Wed, 27 Sep 2017 15:41:05 GMT

New page: '''Unreleased structure''' The entry 5xqk is ON HOLD until Paper Publication Authors: Li, T.L., Hsu, N.S., Wang, Y.L. Description: Crystal Structure of Transketolase in complex with xy...

New page

'''Unreleased structure'''

The entry 5xqk is ON HOLD until Paper Publication

Authors: Li, T.L., Hsu, N.S., Wang, Y.L.

Description: Crystal Structure of Transketolase in complex with xylulose-5-phosphate from Pichia Stipitis
[[Category: Unreleased Structures]]
[[Category: Li, T.L]]
[[Category: Hsu, N.S]]
[[Category: Wang, Y.L]]