2a59: Difference between revisions

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<StructureSection load='2a59' size='340' side='right'caption='[[2a59]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='2a59' size='340' side='right'caption='[[2a59]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2a59]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A59 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2a59]] 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=2A59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A59 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LMZ:5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE'>LMZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kyy|1kyy]], [[2a57|2a57]], [[2a58|2a58]], [[1kyv|1kyv]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LMZ:5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE'>LMZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rib4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></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=2a59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a59 OCA], [https://pdbe.org/2a59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a59 RCSB], [https://www.ebi.ac.uk/pdbsum/2a59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a59 ProSAT]</span></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=2a59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a59 OCA], [https://pdbe.org/2a59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a59 RCSB], [https://www.ebi.ac.uk/pdbsum/2a59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a59 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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>
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2a59 ConSurf].
</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=2a59 ConSurf].
<div style="clear:both"></div>
<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2a59" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
[[Category: Cbs 356]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bacher, A]]
[[Category: Breithaupt, C]]
[[Category: Cushman, M]]
[[Category: Fischer, M]]
[[Category: Gerhardt, S]]
[[Category: Haase, I]]
[[Category: Huber, R]]
[[Category: Koch, M]]
[[Category: Weber, S]]
[[Category: 5-nitroso-6-ribitylamino-2]]
[[Category: 7-dimethyl-8-ribityllumazine synthase]]
[[Category: Lusy]]
[[Category: Mutant w27y]]
[[Category: Schizosaccharomyces pombe]]
[[Category: Schizosaccharomyces pombe]]
[[Category: Transferase]]
[[Category: Bacher A]]
[[Category: Breithaupt C]]
[[Category: Cushman M]]
[[Category: Fischer M]]
[[Category: Gerhardt S]]
[[Category: Haase I]]
[[Category: Huber R]]
[[Category: Koch M]]
[[Category: Weber S]]

Latest revision as of 12:11, 14 February 2024

Structure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedioneStructure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione

Structural highlights

2a59 is a 5 chain structure with sequence from Schizosaccharomyces pombe. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Fischer M, Haase I, Feicht R, Richter G, Gerhardt S, Changeux JP, Huber R, Bacher A. Biosynthesis of riboflavin: 6,7-dimethyl-8-ribityllumazine synthase of Schizosaccharomyces pombe. Eur J Biochem. 2002 Jan;269(2):519-26. PMID:11856310

2a59, resolution 2.70Å

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