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1nqw

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[[Image:1nqw.gif|left|200px]]<br /><applet load="1nqw" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nqw, resolution 2.20&Aring;" />
 
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'''Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid'''<br />
 
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==Overview==
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==Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid==
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6,7-Dimethyl-8-ribityllumazine is the biosynthetic precursor of riboflavin, which, as a coenzyme, plays a vital role in the electron transfer process for energy production in all cellular organisms. The enzymes involved in lumazine biosynthesis have been studied in considerable detail. However, the conclusive mechanism of the reaction catalyzed by lumazine synthase has remained unclear. Here, we report four crystal structures of the enzyme from the hyperthermophilic bacterium Aquifex aeolicus in complex with different inhibitor compounds. The structures were refined at resolutions of 1.72 A, 1.85 A, 2.05 A and 2.2 A, respectively. The inhibitors have been designed in order to mimic the substrate, the putative reaction intermediates and the final product. Structural comparisons of the native enzyme and the inhibitor complexes as well as the kinetic data of single-site mutants of lumazine synthase from Bacillus subtilis showed that several highly conserved residues at the active site, namely Phe22, His88, Arg127, Lys135 and Glu138 are most likely involved in catalysis. A structural model of the catalytic process, which illustrates binding of substrates, enantiomer specificity, proton abstraction/donation, inorganic phosphate elimination, formation of the Schiff base and cyclization is proposed.
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<StructureSection load='1nqw' size='340' side='right'caption='[[1nqw]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1nqw]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NQW FirstGlance]. <br>
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1NQW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with <scene name='pdbligand=5YL:'>5YL</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=1NQW 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]] 2.2&#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=5YL:5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRIMIDINEDIONE-5-YL)+PENTYL-1-PHOSPHONIC+ACID'>5YL</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=1nqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nqw OCA], [https://pdbe.org/1nqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nqw RCSB], [https://www.ebi.ac.uk/pdbsum/1nqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nqw ProSAT]</span></td></tr>
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A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus., Zhang X, Meining W, Cushman M, Haase I, Fischer M, Bacher A, Ladenstein R, J Mol Biol. 2003 Apr 18;328(1):167-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12684006 12684006]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RISB_AQUAE RISB_AQUAE] 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:12603336</ref> <ref>PMID:11237620</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/nq/1nqw_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=1nqw 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>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Riboflavin synthase]]
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[[Category: Large Structures]]
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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: Haase I]]
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[[Category: Haase, I.]]
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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: Zhang X]]
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[[Category: Zhang, X.]]
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[[Category: 5YL]]
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[[Category: aquifex aeolicus]]
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[[Category: catalytic mechanism]]
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[[Category: inhibitor complex]]
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[[Category: lumazine synthase]]
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[[Category: vitamin biosynthesis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:09:03 2008''
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Current revision

Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid

PDB ID 1nqw

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