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| | <StructureSection load='6sgn' size='340' side='right'caption='[[6sgn]], [[Resolution|resolution]] 2.50Å' scene=''> | | <StructureSection load='6sgn' size='340' side='right'caption='[[6sgn]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6sgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SGN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6sgn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SGN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LD8:2,4-dimethoxypyrimidine'>LD8</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]] 2.501Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6sgg|6sgg]], [[6sgj|6sgj]], [[6sgl|6sgl]], [[6sgm|6sgm]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LD8:2,4-dimethoxypyrimidine'>LD8</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rutA, ycdM, b1012, JW0997 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6sgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sgn OCA], [https://pdbe.org/6sgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sgn RCSB], [https://www.ebi.ac.uk/pdbsum/6sgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sgn ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.46 1.14.99.46] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6sgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sgn OCA], [http://pdbe.org/6sgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sgn RCSB], [http://www.ebi.ac.uk/pdbsum/6sgn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sgn ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RUTA_ECOLI RUTA_ECOLI]] Catalyzes the pyrimidine ring opening between N-3 and C-4 by an unusual flavin hydroperoxide-catalyzed mechanism to yield ureidoacrylate peracid. It cleaves pyrmidine rings directly by adding oxygen atoms, making a toxic ureidoacrylate peracid product which can be spontaneously reduced to ureidoacrylate. Requires the flavin reductase RutF to regenerate FMN in vivo. RutF can be substituted by Fre in vitro.<ref>PMID:16540542</ref> <ref>PMID:20400551</ref> | + | [https://www.uniprot.org/uniprot/RUTA_ECOLI RUTA_ECOLI] Catalyzes the pyrimidine ring opening between N-3 and C-4 by an unusual flavin hydroperoxide-catalyzed mechanism to yield ureidoacrylate peracid. It cleaves pyrmidine rings directly by adding oxygen atoms, making a toxic ureidoacrylate peracid product which can be spontaneously reduced to ureidoacrylate. Requires the flavin reductase RutF to regenerate FMN in vivo. RutF can be substituted by Fre in vitro.<ref>PMID:16540542</ref> <ref>PMID:20400551</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Oxidoreductase]]
| + | [[Category: Matthews A]] |
| - | [[Category: Matthews, A]] | + | [[Category: Saleem-Batcha R]] |
| - | [[Category: Saleem-Batcha, R]] | + | [[Category: Teufel R]] |
| - | [[Category: Teufel, R]] | + | |
| - | [[Category: Bioengineering]]
| + | |
| - | [[Category: Flavin-n5-oxide]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Fmn]]
| + | |
| - | [[Category: Monooxygenase]]
| + | |
| - | [[Category: Ruta]]
| + | |
| Structural highlights
Function
RUTA_ECOLI Catalyzes the pyrimidine ring opening between N-3 and C-4 by an unusual flavin hydroperoxide-catalyzed mechanism to yield ureidoacrylate peracid. It cleaves pyrmidine rings directly by adding oxygen atoms, making a toxic ureidoacrylate peracid product which can be spontaneously reduced to ureidoacrylate. Requires the flavin reductase RutF to regenerate FMN in vivo. RutF can be substituted by Fre in vitro.[1] [2]
Publication Abstract from PubMed
One of the hallmark reactions catalyzed by flavin-dependent enzymes is the incorporation of an oxygen atom derived from dioxygen into organic substrates. For many decades, these flavin monooxygenases were assumed to use exclusively the flavin-C4a-(hydro)peroxide as their oxygen-transferring intermediate. We demonstrate that flavoenzymes may instead employ a flavin-N5-peroxide as a soft alpha-nucleophile for catalysis, which enables chemistry not accessible to canonical monooxygenases. This includes, for example, the redox-neutral cleavage of carbon-hetero bonds or the dehalogenation of inert environmental pollutants via atypical oxygenations. We furthermore identify a shared structural motif for dioxygen activation and N5-functionalization, suggesting a conserved pathway that may be operative in numerous characterized and uncharacterized flavoenzymes from diverse organisms. Our findings show that overlooked flavin-N5-oxygen adducts are more widespread and may facilitate versatile chemistry, thus upending the notion that flavin monooxygenases exclusively function as nature's equivalents to organic peroxides in synthetic chemistry.
Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases.,Matthews A, Saleem-Batcha R, Sanders JN, Stull F, Houk KN, Teufel R Nat Chem Biol. 2020 May;16(5):556-563. doi: 10.1038/s41589-020-0476-2. Epub 2020 , Feb 17. PMID:32066967[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, Kustu S. A previously undescribed pathway for pyrimidine catabolism. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15. PMID:16540542 doi:0600521103
- ↑ Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE. The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J Bacteriol. 2010 Aug;192(16):4089-102. doi: 10.1128/JB.00201-10. Epub 2010 Apr, 16. PMID:20400551 doi:http://dx.doi.org/10.1128/JB.00201-10
- ↑ Matthews A, Saleem-Batcha R, Sanders JN, Stull F, Houk KN, Teufel R. Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Nat Chem Biol. 2020 May;16(5):556-563. doi: 10.1038/s41589-020-0476-2. Epub 2020 , Feb 17. PMID:32066967 doi:http://dx.doi.org/10.1038/s41589-020-0476-2
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