1trk

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(New page: 200px<br /><applet load="1trk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1trk, resolution 2.0&Aring;" /> '''REFINED STRUCTURE OF ...)
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[[Image:1trk.jpg|left|200px]]<br /><applet load="1trk" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1trk, resolution 2.0&Aring;" />
 
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'''REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION'''<br />
 
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==Overview==
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==REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION==
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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.
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<StructureSection load='1trk' size='340' side='right'caption='[[1trk]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tr/1trk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1TRK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with CA and TPP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TRK OCA].
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*[[Transketolase 3D structures|Transketolase 3D structures]]
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== References ==
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==Reference==
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<references/>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8176731 8176731]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Lindqvist Y]]
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[[Category: Transketolase]]
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[[Category: Nikkola M]]
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[[Category: Lindqvist, Y.]]
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[[Category: Schneider G]]
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[[Category: Nikkola, M.]]
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[[Category: Schneider, G.]]
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[[Category: CA]]
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[[Category: TPP]]
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[[Category: transferase(ketone residues)]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:32:23 2007''
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REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION

PDB ID 1trk

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