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| | <StructureSection load='2f59' size='340' side='right'caption='[[2f59]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='2f59' size='340' side='right'caption='[[2f59]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2f59]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_of_abortion"_bang_1897 "bacillus of abortion" bang 1897]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F59 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2f59]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_abortus Brucella abortus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F59 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE'>INI</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1di0|1di0]], [[1xn1|1xn1]], [[1t13|1t13]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE'>INI</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ribH1, ribH, ribH-1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235 "Bacillus of abortion" Bang 1897])</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=2f59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f59 OCA], [https://pdbe.org/2f59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f59 RCSB], [https://www.ebi.ac.uk/pdbsum/2f59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f59 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=2f59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f59 OCA], [https://pdbe.org/2f59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f59 RCSB], [https://www.ebi.ac.uk/pdbsum/2f59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f59 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RISB1_BRUAB RISB1_BRUAB]] 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:16923880</ref>
| + | [https://www.uniprot.org/uniprot/RISB1_BRUAB RISB1_BRUAB] 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:16923880</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: Bacillus of abortion bang 1897]] | + | [[Category: Brucella abortus]] |
| - | [[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bacher, A]] | + | [[Category: Bacher A]] |
| - | [[Category: Bonomi, H R]] | + | [[Category: Bonomi HR]] |
| - | [[Category: Braden, B C]] | + | [[Category: Braden BC]] |
| - | [[Category: Fischer, M]] | + | [[Category: Fischer M]] |
| - | [[Category: Goldbaum, F A]] | + | [[Category: Goldbaum FA]] |
| - | [[Category: Guimaraes, B G]] | + | [[Category: Guimaraes BG]] |
| - | [[Category: Haase, I]] | + | [[Category: Haase I]] |
| - | [[Category: Klinke, S]] | + | [[Category: Klinke S]] |
| - | [[Category: Zylberman, V]] | + | [[Category: Zylberman V]] |
| - | [[Category: Enzyme-substrate analogue]]
| + | |
| - | [[Category: Inhibitor complex]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
RISB1_BRUAB 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
- ↑ Zylberman V, Klinke S, Haase I, Bacher A, Fischer M, Goldbaum FA. Evolution of vitamin B2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of Brucella. J Bacteriol. 2006 Sep;188(17):6135-42. PMID:16923880 doi:http://dx.doi.org/10.1128/JB.00207-06
- ↑ 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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