1gpu: Difference between revisions
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==Transketolase intermediate== | |||
<StructureSection load='1gpu' size='340' side='right' caption='[[1gpu]], [[Resolution|resolution]] 1.86Å' scene=''> | ==Transketolase complex with reaction intermediate== | ||
<StructureSection load='1gpu' size='340' side='right'caption='[[1gpu]], [[Resolution|resolution]] 1.86Å' scene=''> | |||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1gpu]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1gpu]] 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=1GPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GPU 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=THD:2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>THD</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.86Å</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=THD:2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>THD</scene></td></tr> | |||
<tr | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpu OCA], [https://pdbe.org/1gpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gpu RCSB], [https://www.ebi.ac.uk/pdbsum/1gpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpu ProSAT]</span></td></tr> | ||
</table> | |||
<table> | == 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> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/1gpu_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/1gpu_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> | ||
</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/ | </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=1gpu ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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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 1gpu" 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: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Fiedler E]] | |||
[[Category: Fiedler | [[Category: Koenig S]] | ||
[[Category: Koenig | [[Category: Sandalova T]] | ||
[[Category: Sandalova | [[Category: Schneider G]] | ||
[[Category: Schneider | [[Category: Thorell S]] | ||
[[Category: Thorell | |||
Latest revision as of 15:03, 13 December 2023
Transketolase complex with reaction intermediateTransketolase complex with reaction intermediate
Structural highlights
FunctionTKT1_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.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedKinetic and spectroscopic data indicated that addition of the donor substrate hydroxypyruvate to the thiamin diphosphate (ThDP)-dependent enzyme transketolase (TK) led to the accumulation of the alpha-carbanion/enamine of (alpha,beta-dihydroxyethyl) ThDP, the key reaction intermediate in enzymatic thiamin catalysis. The three-dimensional structure of this intermediate trapped in the active site of yeast TK was determined to 1.9-A resolution by using cryocrystallography. The electron density suggests a planar alpha-carbanion/enamine intermediate having the E-configuration. The reaction intermediate is firmly held in place through direct hydrogen bonds to His-103 and His-481 and an indirect hydrogen bond via a water molecule to His-69. The 4-NH(2) group of the amino-pyrimidine ring of ThDP is within 3 A distance to the alpha-hydroxy oxygen atom of the dihydroxyethyl moiety but at an angle unfavorable for a strong hydrogen bond. No structural changes occur in TK on formation of the reaction intermediate, suggesting that the active site is poised for catalysis and conformational changes during the enzyme reaction are not very likely. The intermediate is present with high occupancy in both active sites, arguing against previous proposals of half-of-the-sites reactivity in yeast TK. Snapshot of a key intermediate in enzymatic thiamin catalysis: crystal structure of the alpha-carbanion of (alpha,beta-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae.,Fiedler E, Thorell S, Sandalova T, Golbik R, Konig S, Schneider G Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):591-5. Epub 2002 Jan 2. PMID:11773632[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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