1ejb

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[[Image:1ejb.jpg|left|200px]]<br /><applet load="1ejb" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ejb, resolution 1.85&Aring;" />
 
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'''LUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE'''<br />
 
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==Overview==
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==LUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE==
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Lumazine synthase of Saccharomyces cerevisiae is a homopentamer with a molecular weight of 90 kDa. Crystals of the recombinant enzyme with a size of up to 1.6 mm were obtained. The space group is P4(1)2(1)2 with lattice dimensions 82.9 A x 82.9 A x 300.2 A. X-ray diffraction data collected under cryogenic conditions were complete to 1.85 A resolution. The structure of the enzyme in complex with the intermediate analogue, 5-(6-D-ribitylamino-2,4-dihydroxypyrimidine-5-yl)-1-pentyl-p hosphonic acid was solved via molecular replacement using the structure of the Bacillus subtilis enzyme as search model and was refined to a final R-factor of 19.8% (Rfree: 22.5%). The conformation of the active site ligand of the enzyme mimicks that of the Schiff base intermediate of the enzyme-catalyzed reaction. The data enable the reconstruction of the reactant topology during the early steps of the catalytic reaction. Structural determinants, which are likely to be responsible for the inability of the S. cerevisiae enzyme to form icosahedral capsids, will be discussed.
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<StructureSection load='1ejb' size='340' side='right'caption='[[1ejb]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1ejb]] is a 5 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=1EJB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EJB FirstGlance]. <br>
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1EJB 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 <scene name='pdbligand=INJ:'>INJ</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJB OCA].
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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]] 1.85&#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=INJ:5-(6-D-RIBITYLAMINO-2,4-DIHYDROXYPYRIMIDIN-5-YL)-1-PENTYL-PHOSPHONIC+ACID'>INJ</scene></td></tr>
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==Reference==
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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=1ejb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejb OCA], [https://pdbe.org/1ejb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ejb RCSB], [https://www.ebi.ac.uk/pdbsum/1ejb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejb ProSAT]</span></td></tr>
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The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue., Meining W, Mortl S, Fischer M, Cushman M, Bacher A, Ladenstein R, J Mol Biol. 2000 May 26;299(1):181-97. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10860731 10860731]
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</table>
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[[Category: Riboflavin synthase]]
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== Function ==
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[https://www.uniprot.org/uniprot/RIB4_YEAST RIB4_YEAST] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:7559556</ref> <ref>PMID:8969176</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/ej/1ejb_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=1ejb ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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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: Bacher A]]
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[[Category: Bacher, A.]]
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[[Category: Cushman M]]
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[[Category: Cushman, M.]]
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[[Category: Fischer M]]
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[[Category: Fischer, M.]]
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[[Category: Ladenstein R]]
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[[Category: Ladenstein, R.]]
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[[Category: Meining W]]
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[[Category: Meining, W.]]
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[[Category: Mortl S]]
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[[Category: Mortl, S.]]
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[[Category: INJ]]
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[[Category: inhibitor complex]]
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[[Category: lumazine synthase]]
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[[Category: saccharomyces cerevisiae]]
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[[Category: vitamin biosynthesis]]
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[[Category: x-ray structure analysis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:28:24 2008''
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Current revision

LUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE

PDB ID 1ejb

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