1kz4

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{{Seed}}
 
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[[Image:1kz4.png|left|200px]]
 
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==Mutant enzyme W63Y Lumazine Synthase from S.pombe==
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The line below this paragraph, containing "STRUCTURE_1kz4", creates the "Structure Box" on the page.
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<StructureSection load='1kz4' size='340' side='right'caption='[[1kz4]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1kz4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KZ4 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 3.1&#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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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{{STRUCTURE_1kz4| PDB=1kz4 | SCENE= }}
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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=1kz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz4 OCA], [https://pdbe.org/1kz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kz4 RCSB], [https://www.ebi.ac.uk/pdbsum/1kz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kz4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RIB4_SCHPO RIB4_SCHPO] 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. Also binds riboflavin with an unexpected high affinity.<ref>PMID:11856310</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/kz/1kz4_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=1kz4 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Riboflavin is an essential cofactor in all organisms. Its direct biosynthetic precursor, 6,7-dimethyl-8-ribityllumazine, is synthesised by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. Recently, we have found that the enzyme from Schizosaccharomyces pombe binds riboflavin, the final product of the pathway with a relatively high affinity with a KD of 1.2 microM. Here, we report on the crystal structure of lumazine synthase from S. pombe with bound riboflavin and compare the binding mode with those of the substrate analogue inhibitor 5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione and of the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine. In all complexes the pyrimidinedione moieties of each respective ligand bind in a very similar orientation. Binding of riboflavin additionally involves a stacking interaction of the dimethylbenzene moiety with the side-chain of His94, a highly conserved residue in all lumazine synthases. The enzyme from Bacillus subtilis showed a KD of at least 1 mM whereas the very homologous enzyme from Saccharomyces cerevisiae had a comparable KD of 3.9 microM. Structural comparison of the S. cerevisiae, the S. pombe, and the mutant enzymes suggests that fine tuning of affinity is achieved by influencing this stacking interaction.
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===Mutant enzyme W63Y Lumazine Synthase from S.pombe===
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The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.,Gerhardt S, Haase I, Steinbacher S, Kaiser JT, Cushman M, Bacher A, Huber R, Fischer M J Mol Biol. 2002 May 17;318(5):1317-29. PMID:12083520<ref>PMID:12083520</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_12083520}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1kz4" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 12083520 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12083520}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1KZ4 is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ4 OCA].
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==Reference==
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<ref group="xtra">PMID:12083520</ref><references group="xtra"/>
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[[Category: Riboflavin synthase]]
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[[Category: Schizosaccharomyces pombe]]
[[Category: Schizosaccharomyces pombe]]
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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: Gerhardt, S.]]
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[[Category: Gerhardt S]]
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[[Category: Haase, I.]]
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[[Category: Haase I]]
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[[Category: Huber, R.]]
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[[Category: Huber R]]
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[[Category: Kaiser, J T.]]
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[[Category: Kaiser JT]]
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[[Category: Steinbacher, S.]]
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[[Category: Steinbacher S]]
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[[Category: Crystal structure]]
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[[Category: Ligand binding]]
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[[Category: Lumazine synthase]]
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[[Category: Riboflavin biosynthesis]]
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[[Category: Schizosaccharomyces pombe]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:12:06 2009''
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Current revision

Mutant enzyme W63Y Lumazine Synthase from S.pombe

PDB ID 1kz4

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