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| | <StructureSection load='2obx' size='340' side='right'caption='[[2obx]], [[Resolution|resolution]] 2.53Å' scene=''> | | <StructureSection load='2obx' size='340' side='right'caption='[[2obx]], [[Resolution|resolution]] 2.53Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2obx]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33669 Atcc 33669]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OBX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2obx]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OBX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE'>INI</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]] 2.53Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t13|1t13]], [[1di0|1di0]], [[1xn1|1xn1]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE'>INI</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">ribH1, ribH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381 ATCC 33669])</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=2obx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obx OCA], [https://pdbe.org/2obx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2obx RCSB], [https://www.ebi.ac.uk/pdbsum/2obx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2obx 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=2obx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obx OCA], [https://pdbe.org/2obx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2obx RCSB], [https://www.ebi.ac.uk/pdbsum/2obx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2obx ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RISB1_RHILO RISB1_RHILO]] 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:17854827</ref>
| + | [https://www.uniprot.org/uniprot/RISB2_RHILO RISB2_RHILO] 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:17854827</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 6,7-dimethyl-8-ribityllumazine synthase]] | |
| - | [[Category: Atcc 33669]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bacher, A]] | + | [[Category: Mesorhizobium loti]] |
| - | [[Category: Bonomi, H R]] | + | [[Category: Bacher A]] |
| - | [[Category: Braden, B C]] | + | [[Category: Bonomi HR]] |
| - | [[Category: Fischer, M]] | + | [[Category: Braden BC]] |
| - | [[Category: Goldbaum, F A]] | + | [[Category: Fischer M]] |
| - | [[Category: Guimaraes, B G]] | + | [[Category: Goldbaum FA]] |
| - | [[Category: Haase, I]] | + | [[Category: Guimaraes BG]] |
| - | [[Category: Klinke, S]] | + | [[Category: Haase I]] |
| - | [[Category: Zylberman, V]] | + | [[Category: Klinke S]] |
| - | [[Category: Alpha-beta]]
| + | [[Category: Zylberman V]] |
| - | [[Category: Lumazine synthase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
RISB2_RHILO 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.[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
6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase; LS) catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. This protein is known to exhibit different quaternary assemblies between species, existing as free pentamers, decamers (dimers of pentamers) and icosahedrally arranged dodecamers of pentamers. A phylogenetic analysis on eubacterial, fungal and plant LSs allowed us to classify them into two categories: Type I LSs (pentameric or icosahedral) and Type II LSs (decameric). The Rhizobiales represent an order of alpha-proteobacteria that includes, among others, the genera Mesorhizobium, Agrobacterium and Brucella. Here, we present structural and kinetic studies on several LSs from Rhizobiales. Interestingly, Mesorhizobium and Brucella encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. We show that Type II LSs appear to be almost inactive, whereas Type I LSs present a highly variable catalytic activity according to the genus. Additionally, we have solved four RibH1/RibH2 crystallographic structures from the genera Mesorhizobium and Brucella. The relationship between the active-site architecture and catalytic properties in these isoenzymes is discussed, and a model that describes the enzymatic behavior is proposed. Furthermore, sequence alignment studies allowed us to extend our results to the genus Agrobacterium. Our results suggest that the selective pressure controlling the riboflavin pathway favored the evolution of catalysts with low reaction rates, since the excess of flavins in the intracellular pool in Rhizobiales could act as a negative factor when these bacteria are exposed to oxidative or nitrosative stress.
Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales.,Klinke S, Zylberman V, Bonomi HR, Haase I, Guimaraes BG, Braden BC, Bacher A, Fischer M, Goldbaum FA J Mol Biol. 2007 Oct 26;373(3):664-80. Epub 2007 Aug 21. PMID:17854827[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Klinke S, Zylberman V, Bonomi HR, Haase I, Guimaraes BG, Braden BC, Bacher A, Fischer M, Goldbaum FA. Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales. J Mol Biol. 2007 Oct 26;373(3):664-80. Epub 2007 Aug 21. PMID:17854827 doi:10.1016/j.jmb.2007.08.021
- ↑ Klinke S, Zylberman V, Bonomi HR, Haase I, Guimaraes BG, Braden BC, Bacher A, Fischer M, Goldbaum FA. Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales. J Mol Biol. 2007 Oct 26;373(3):664-80. Epub 2007 Aug 21. PMID:17854827 doi:10.1016/j.jmb.2007.08.021
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