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2r8o

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[[Image:2r8o.jpg|left|200px]]<br /><applet load="2r8o" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2r8o, resolution 1.470&Aring;" />
 
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'''Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate'''<br />
 
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==Overview==
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==Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate==
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Transketolase is a prominent thiamin diphosphate-dependent enzyme in sugar metabolism that catalyzes the reversible transfer of a 2-carbon dihydroxyethyl fragment between a donor ketose and an acceptor aldose. The X-ray structures of transketolase from E. coli in a covalent complex with donor ketoses d-xylulose 5-phosphate (X5P) and d-fructose 6-phosphate (F6P) at 1.47 A and 1.65 A resolution reveal significant strain in the tetrahedral cofactor-sugar adducts with a 25-30 degrees out-of-plane distortion of the C2-Calpha bond connecting the substrates' carbonyl with the C2 of the cofactor's thiazolium part. Both intermediates adopt very similar extended conformations in the active site with a perpendicular orientation of the scissile C2-C3 sugar bond relative to the thiazolium ring. The sugar-derived hydroxyl groups of the intermediates form conserved hydrogen bonds with one Asp side chain, with a cluster of His residues and with the N4' of the aminopyrimidine ring of the cofactor. The phosphate moiety is held in place by electrostatic and hydrogen-bonding interactions with Arg, His, and Ser side chains. With the exception of the thiazolium part of the cofactor, no structural changes are observable during intermediate formation indicating that the active site is poised for catalysis. DFT calculations on both X5P-thiamin and X5P-thiazolium models demonstrate that an out-of-plane distortion of the C2-Calpha bond is energetically more favorable than a coplanar bond. The X-ray structure with the acceptor aldose d-ribose 5-phosphate (R5P) noncovalently bound in the active site suggests that the sugar is present in multiple forms: in a strained ring-closed beta-d-furanose form in C2-exo conformation as well as in an extended acyclic aldehyde form, with the reactive C1 aldo function held close to Calpha of the presumably planar carbanion/enamine intermediate. The latter form of R5P may be viewed as a near attack conformation. The R5P binding site overlaps with those of the leaving group moieties of the covalent donor-cofactor adducts, demonstrating that R5P directly competes with the donor-derived products glyceraldehyde 3-phosphate and erythrose 4-phosphate, which are substrates of the reverse reaction, for the same docking site at the active site and reaction with the DHEThDP enamine.
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<StructureSection load='2r8o' size='340' side='right'caption='[[2r8o]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2r8o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8O 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]] 1.47&#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=EDO:1,2-ETHANEDIOL'>EDO</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>
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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=2r8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8o OCA], [https://pdbe.org/2r8o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8o RCSB], [https://www.ebi.ac.uk/pdbsum/2r8o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8o ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TKT1_ECOLI TKT1_ECOLI] Catalyzes the reversible transfer of a two-carbon ketol group from sedoheptulose-7-phosphate to glyceraldehyde-3-phosphate, producing xylulose-5-phosphate and ribose-5-phosphate. 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:17914867</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/r8/2r8o_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=2r8o 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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2R8O is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=T5X:'>T5X</scene> and <scene name='pdbligand=EDO:'>EDO</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8O OCA].
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*[[Transketolase|Transketolase]]
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*[[Transketolase 3D structures|Transketolase 3D structures]]
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==Reference==
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== References ==
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Strain and near attack conformers in enzymic thiamin catalysis: X-ray crystallographic snapshots of bacterial transketolase in covalent complex with donor ketoses xylulose 5-phosphate and fructose 6-phosphate, and in noncovalent complex with acceptor aldose ribose 5-phosphate., Asztalos P, Parthier C, Golbik R, Kleinschmidt M, Hubner G, Weiss MS, Friedemann R, Wille G, Tittmann K, Biochemistry. 2007 Oct 30;46(43):12037-52. Epub 2007 Oct 3. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17914867 17914867]
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<references/>
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[[Category: Escherichia coli]]
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__TOC__
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[[Category: Single protein]]
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</StructureSection>
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[[Category: Transketolase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Asztalos, P.]]
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[[Category: Large Structures]]
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[[Category: Tittmann, K.]]
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[[Category: Asztalos P]]
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[[Category: Weiss, M S.]]
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[[Category: Tittmann K]]
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[[Category: Wille, G.]]
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[[Category: Weiss MS]]
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[[Category: CA]]
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[[Category: Wille G]]
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[[Category: EDO]]
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[[Category: T5X]]
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[[Category: calcium]]
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[[Category: metal-binding]]
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[[Category: reaction intermediate]]
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[[Category: thiamine pyrophosphate]]
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[[Category: transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:45:28 2008''
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Current revision

Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate

PDB ID 2r8o

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