2a57: Difference between revisions
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< | ==Structure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 6-carboxyethyl-7-oxo-8-ribityllumazine== | ||
<StructureSection load='2a57' size='340' side='right'caption='[[2a57]], [[Resolution|resolution]] 2.75Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2a57]] 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=2A57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A57 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.75Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRM:3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC+ACID'>CRM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a57 OCA], [https://pdbe.org/2a57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a57 RCSB], [https://www.ebi.ac.uk/pdbsum/2a57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a57 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a5/2a57_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=2a57 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The amino acid residue tryptophan 27 of 6,7-dimethyl-8-ribityllumazine synthase of the yeast Schizosaccharomyces pombe was replaced by tyrosine. The structures of the W27Y mutant protein in complex with riboflavin, the substrate analogue 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, and the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine, were determined by X-ray crystallography at resolutions of 2.7-2.8 A. Whereas the indole system of W27 forms a coplanar pi-complex with riboflavin, the corresponding phenyl ring in the W27Y mutant establishes only peripheral contact with the heterocyclic ring system of the bound riboflavin. These findings provide an explanation for the absence of the long wavelength shift in optical absorption spectra of riboflavin bound to the mutant enzyme. The structures of the mutants are important tools for the interpretation of the unusual physical properties of riboflavin in complex with lumazine synthase. | |||
Structural basis of charge transfer complex formation by riboflavin bound to 6,7-dimethyl-8-ribityllumazine synthase.,Koch M, Breithaupt C, GerhardtHaase S, Weber S, Cushman M, Huber R, Bacher A, Fischer M Eur J Biochem. 2004 Aug;271(15):3208-14. PMID:15265040<ref>PMID:15265040</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2a57" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
[[Category: | |||
[[Category: Schizosaccharomyces pombe]] | [[Category: Schizosaccharomyces pombe]] | ||
[[Category: Bacher A]] | |||
[[Category: Bacher | [[Category: Breithaupt C]] | ||
[[Category: Breithaupt | [[Category: Cushman M]] | ||
[[Category: Cushman | [[Category: Fischer M]] | ||
[[Category: Fischer | [[Category: Gerhardt S]] | ||
[[Category: Gerhardt | [[Category: Haase I]] | ||
[[Category: Haase | [[Category: Huber R]] | ||
[[Category: Huber | [[Category: Koch M]] | ||
[[Category: Koch | [[Category: Weber S]] | ||
[[Category: Weber | |||
Latest revision as of 10:19, 23 August 2023
Structure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 6-carboxyethyl-7-oxo-8-ribityllumazineStructure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 6-carboxyethyl-7-oxo-8-ribityllumazine
Structural highlights
FunctionRIB4_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.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe amino acid residue tryptophan 27 of 6,7-dimethyl-8-ribityllumazine synthase of the yeast Schizosaccharomyces pombe was replaced by tyrosine. The structures of the W27Y mutant protein in complex with riboflavin, the substrate analogue 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, and the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine, were determined by X-ray crystallography at resolutions of 2.7-2.8 A. Whereas the indole system of W27 forms a coplanar pi-complex with riboflavin, the corresponding phenyl ring in the W27Y mutant establishes only peripheral contact with the heterocyclic ring system of the bound riboflavin. These findings provide an explanation for the absence of the long wavelength shift in optical absorption spectra of riboflavin bound to the mutant enzyme. The structures of the mutants are important tools for the interpretation of the unusual physical properties of riboflavin in complex with lumazine synthase. Structural basis of charge transfer complex formation by riboflavin bound to 6,7-dimethyl-8-ribityllumazine synthase.,Koch M, Breithaupt C, GerhardtHaase S, Weber S, Cushman M, Huber R, Bacher A, Fischer M Eur J Biochem. 2004 Aug;271(15):3208-14. PMID:15265040[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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