1trk - Revision history

OCA at 08:41, 14 February 2024

OCA — Wed, 14 Feb 2024 08:41:30 GMT

←Older revision		Revision as of 08:41, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1trk' size='340' side='right'caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1trk' size='340' side='right'caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRK FirstGlance]. <br>
-	</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=TPP:THIAMINE+DIPHOSPHATE'>TPP</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Transketolase Transketolase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.1 2.2.1.1]~~ </~~span~~></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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [https://pdbe.org/1trk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [https://www.ebi.ac.uk/pdbsum/1trk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1trk ProSAT]</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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [https://pdbe.org/1trk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [https://www.ebi.ac.uk/pdbsum/1trk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1trk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TKT1_YEAST TKT1_YEAST]] 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.<ref>PMID:8521838</ref>	+	[https://www.uniprot.org/uniprot/TKT1_YEAST TKT1_YEAST] 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.<ref>PMID:8521838</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1trk ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1trk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of transketolase from Saccharomyces cerevisiae has been refined to a crystallographic residual of 15.7% at 2.0 A resolution using the program package X-PLOR. The refined model of the transketolase homodimer, corresponding to 1356 amino acid residues in the asymmetric unit, consists of 10,396 protein atoms, 1040 solvent molecules, 52 thiamine diphosphate atoms and two calcium ions. All amino acid residues except for the two N-terminal residues of the two subunits are defined in the electron density maps and refined. The estimated root-mean-square (r.m.s.) error of the model is less than 0.2 A as deduced from Luzzati plots. The r.m.s. deviation from ideality is 0.017 A for bond distances and 3.1 degrees for bond angles. The main-chain torsion angles of non-glycine residues lie within the allowed regions of the Ramachandran plots. The model shows a very good fit to the electron density maps. The average B-factor for all protein atoms in the first subunit is 19 A2, and 15A2 in the second. The average B-factor for solvent atoms is 32A2. The two subunits of transketolase were refined independently and have nearly identical structures with an r.m.s. deviation of 0.24 A for C alpha atoms 3 to 680, and slightly less when aligning the individual domains. A few exceptions from the 2-fold symmetry are found, mostly in the surface residues. The thiamine diphosphate cofactors have identical conformations. The cofactor is shielded from solvent except for the C-2 atom of the thiazolium ring. A calcium ion is bound to the diphosphate group of thiamine and protein ligands. The metal binding site and the interactions of thiamine diphosphate with protein residues are described. A network of hydrogen bonds consisting of glutamic acid residues and internal water molecules connects the two thiamine diphosphate molecules. Its structure and possible functional implications are discussed.
-
-	Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution.,Nikkola M, Lindqvist Y, Schneider G J Mol Biol. 1994 May 6;238(3):387-404. PMID:8176731<ref>PMID:8176731</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1trk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Transketolase\|Transketolase]]	+	*[[Transketolase 3D structures\|Transketolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Transketolase~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Lindqvist, Y]]	+	[[Category: Lindqvist Y]]
-	[[Category: Nikkola, M]]	+	[[Category: Nikkola M]]
-	[[Category: Schneider, G]]	+	[[Category: Schneider G]]

OCA at 09:31, 29 September 2021

OCA — Wed, 29 Sep 2021 09:31:35 GMT

←Older revision		Revision as of 09:31, 29 September 2021
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	<StructureSection load='1trk' size='340' side='right'caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1trk' size='340' side='right'caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TRK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRK 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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>	+	</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=TPP:THIAMINE+DIPHOSPHATE'>TPP</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Transketolase Transketolase], with EC number [https://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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [~~http~~://pdbe.org/1trk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1trk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1trk ProSAT]</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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [https://pdbe.org/1trk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [https://www.ebi.ac.uk/pdbsum/1trk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1trk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TKT1_YEAST TKT1_YEAST]] 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.<ref>PMID:8521838</ref>	+	[[https://www.uniprot.org/uniprot/TKT1_YEAST TKT1_YEAST]] 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.<ref>PMID:8521838</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:00, 25 December 2019

OCA — Wed, 25 Dec 2019 14:00:06 GMT

←Older revision		Revision as of 14:00, 25 December 2019
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	==REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION==		==REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION==
-	<StructureSection load='1trk' size='340' side='right' caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1trk' size='340' side='right'caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRK FirstGlance]. <br>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Transketolase]]		[[Category: Transketolase]]
	[[Category: Lindqvist, Y]]		[[Category: Lindqvist, Y]]
	[[Category: Nikkola, M]]		[[Category: Nikkola, M]]
	[[Category: Schneider, G]]		[[Category: Schneider, G]]

OCA at 08:49, 21 March 2018

OCA — Wed, 21 Mar 2018 08:49:58 GMT

←Older revision		Revision as of 08:49, 21 March 2018
Line 1:		Line 1:
		+
	==REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION==		==REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION==
	<StructureSection load='1trk' size='340' side='right' caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1trk' size='340' side='right' caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 5:		Line 6:
	</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=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=TPP:THIAMINE+DIPHOSPHATE'>TPP</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='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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [http://pdbe.org/1trk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [http://www.ebi.ac.uk/pdbsum/1trk PDBsum]</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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [http://pdbe.org/1trk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [http://www.ebi.ac.uk/pdbsum/1trk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1trk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tr/1trk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tr/1trk_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 13:41, 9 February 2016

OCA — Tue, 09 Feb 2016 13:41:29 GMT

←Older revision		Revision as of 13:41, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1trk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:47, 10 September 2015

OCA — Thu, 10 Sep 2015 22:47:19 GMT

←Older revision		Revision as of 22:47, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1trk' size='340' side='right' caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1trk' size='340' side='right' caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRK 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=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=TPP:THIAMINE+DIPHOSPHATE'>TPP</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='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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [http://www.ebi.ac.uk/pdbsum/1trk PDBsum]</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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [http://pdbe.org/1trk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [http://www.ebi.ac.uk/pdbsum/1trk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1trk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Transketolase]]		[[Category: Transketolase]]
	[[Category: Lindqvist, Y]]		[[Category: Lindqvist, Y]]
	[[Category: Nikkola, M]]		[[Category: Nikkola, M]]
	[[Category: Schneider, G]]		[[Category: Schneider, G]]

OCA at 07:09, 25 December 2014

OCA — Thu, 25 Dec 2014 07:09:35 GMT

←Older revision		Revision as of 07:09, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene><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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [http://www.ebi.ac.uk/pdbsum/1trk PDBsum]</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=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [http://www.ebi.ac.uk/pdbsum/1trk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TKT1_YEAST TKT1_YEAST]] 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.<ref>PMID:8521838</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Transketolase]]		[[Category: Transketolase]]
-	[[Category: Lindqvist, Y.]]	+	[[Category: Lindqvist, Y]]
-	[[Category: Nikkola, M.]]	+	[[Category: Nikkola, M]]
-	[[Category: Schneider, G.]]	+	[[Category: Schneider, G]]

OCA at 19:44, 28 September 2014

OCA — Sun, 28 Sep 2014 19:44:06 GMT

←Older revision		Revision as of 19:44, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1trk.~~png\|left~~\|200px]]	+	==REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION==
		+	<StructureSection load='1trk' size='340' side='right' caption='[[1trk]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene><br>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1trk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1trk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1trk RCSB], [http://www.ebi.ac.uk/pdbsum/1trk PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tr/1trk_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of transketolase from Saccharomyces cerevisiae has been refined to a crystallographic residual of 15.7% at 2.0 A resolution using the program package X-PLOR. The refined model of the transketolase homodimer, corresponding to 1356 amino acid residues in the asymmetric unit, consists of 10,396 protein atoms, 1040 solvent molecules, 52 thiamine diphosphate atoms and two calcium ions. All amino acid residues except for the two N-terminal residues of the two subunits are defined in the electron density maps and refined. The estimated root-mean-square (r.m.s.) error of the model is less than 0.2 A as deduced from Luzzati plots. The r.m.s. deviation from ideality is 0.017 A for bond distances and 3.1 degrees for bond angles. The main-chain torsion angles of non-glycine residues lie within the allowed regions of the Ramachandran plots. The model shows a very good fit to the electron density maps. The average B-factor for all protein atoms in the first subunit is 19 A2, and 15A2 in the second. The average B-factor for solvent atoms is 32A2. The two subunits of transketolase were refined independently and have nearly identical structures with an r.m.s. deviation of 0.24 A for C alpha atoms 3 to 680, and slightly less when aligning the individual domains. A few exceptions from the 2-fold symmetry are found, mostly in the surface residues. The thiamine diphosphate cofactors have identical conformations. The cofactor is shielded from solvent except for the C-2 atom of the thiazolium ring. A calcium ion is bound to the diphosphate group of thiamine and protein ligands. The metal binding site and the interactions of thiamine diphosphate with protein residues are described. A network of hydrogen bonds consisting of glutamic acid residues and internal water molecules connects the two thiamine diphosphate molecules. Its structure and possible functional implications are discussed.

-	~~{{STRUCTURE_1trk\| PDB=1trk \| SCENE= }}~~	+	Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution.,Nikkola M, Lindqvist Y, Schneider G J Mol Biol. 1994 May 6;238(3):387-404. PMID:8176731<ref>PMID:8176731</ref>

-	~~===REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8176731}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1trk]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA].~~	+

	==See Also==		==See Also==
	*[[Transketolase\|Transketolase]]		*[[Transketolase\|Transketolase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008176731<~~/~~ref~~><~~ref group="xtra">PMID:011170211</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Transketolase]]		[[Category: Transketolase]]

OCA at 14:01, 20 October 2012

OCA — Sat, 20 Oct 2012 14:01:16 GMT

←Older revision		Revision as of 14:01, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1trk]] is a 2 chain structure ~~of [[Transketolase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA].	+	[[1trk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA].

	==See Also==		==See Also==

OCA: Protected "1trk" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 13:48:47 GMT

Protected "1trk" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:48, 26 July 2012