1nqw: Difference between revisions

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-[[Image:1nqw.gif|left|200px]]
-<!--
+==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==
-The line below this paragraph, containing "STRUCTURE_1nqw", creates the "Structure Box" on the page.
+<StructureSection load='1nqw' size='340' side='right'caption='[[1nqw]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<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>
-{{STRUCTURE_1nqw|  PDB=1nqw  |  SCENE=  }}
+<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>
+</table>
-'''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'''
+== Function ==
+[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>
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-,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.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nq/1nqw_consurf.spt"</scriptWhenChecked>
-NQW is a [[Single protein]] structure of sequence from [http://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].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-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://www.ncbi.nlm.nih.gov/pubmed/12684006 12684006]
+</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].
-[[Category: Aquifex aeolicus]]
+<div style="clear:both"></div>
-[[Category: Riboflavin synthase]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Bacher, A.]]
+__TOC__
-[[Category: Cushman, M.]]
+</StructureSection>
-[[Category: Fischer, M.]]
-[[Category: Haase, I.]]
-[[Category: Ladenstein, R.]]
-[[Category: Meining, W.]]
-[[Category: Zhang, X.]]
 [[Category: Aquifex aeolicus]]
-[[Category: Catalytic mechanism]]
+[[Category: Large Structures]]
-[[Category: Inhibitor complex]]
+[[Category: Bacher A]]
-[[Category: Lumazine synthase]]
+[[Category: Cushman M]]
-[[Category: Vitamin biosynthesis]]
+[[Category: Fischer M]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:52:26 2008''
+[[Category: Haase I]]
+[[Category: Ladenstein R]]
+[[Category: Meining W]]
+[[Category: Zhang X]]