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| | <StructureSection load='1kyx' size='340' side='right'caption='[[1kyx]], [[Resolution|resolution]] 2.60Å' scene=''> | | <StructureSection load='1kyx' size='340' side='right'caption='[[1kyx]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1kyx]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KYX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KYX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1kyx]] 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=1KYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KYX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kyv|1kyv]], [[1kyy|1kyy]], [[1kz1|1kz1]], [[1kz4|1kz4]], [[1kz6|1kz6]], [[1kz9|1kz9]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kyv|1kyv]], [[1kyy|1kyy]], [[1kz1|1kz1]], [[1kz4|1kz4]], [[1kz6|1kz6]], [[1kz9|1kz9]]</div></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kyx OCA], [http://pdbe.org/1kyx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kyx RCSB], [http://www.ebi.ac.uk/pdbsum/1kyx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kyx 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=1kyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kyx OCA], [https://pdbe.org/1kyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kyx RCSB], [https://www.ebi.ac.uk/pdbsum/1kyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kyx ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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]] |
| Structural highlights
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.
Publication Abstract from PubMed
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.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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
- ↑ Gerhardt S, Haase I, Steinbacher S, Kaiser JT, Cushman M, Bacher A, Huber R, Fischer M. The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase. J Mol Biol. 2002 May 17;318(5):1317-29. PMID:12083520
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