6a4h: Difference between revisions

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 <StructureSection load='6a4h' size='340' side='right'caption='[[6a4h]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6a4h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A4H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6a4h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A4H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9QF:[(2~{R},3~{S},4~{S})-5-[(4~{a}~{S})-4~{a}-(dioxidanyl)-7,8-dimethyl-2,4-bis(oxidanylidene)-5~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+dihydrogen+phosphate'>9QF</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]] 1.99&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxymandelate_oxidase 4-hydroxymandelate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.46 1.1.3.46] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9QF:[(2~{R},3~{S},4~{S})-5-[(4~{a}~{S})-4~{a}-(dioxidanyl)-7,8-dimethyl-2,4-bis(oxidanylidene)-5~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+dihydrogen+phosphate'>9QF</scene></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=6a4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4h OCA], [http://pdbe.org/6a4h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a4h RCSB], [http://www.ebi.ac.uk/pdbsum/6a4h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4h 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=6a4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4h OCA], [https://pdbe.org/6a4h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a4h RCSB], [https://www.ebi.ac.uk/pdbsum/6a4h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4h ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HMO_AMYOR HMO_AMYOR]] Catalyzes the oxidation of p-hydroxymandelate to p-hydroxybenzoylformate in the biosynthesis of L-(4-hydroxyphenyl)glycine and L-(3,5-dihydroxyphenyl)glycine, 2 non-proteinogenic amino acids occurring in the vancomycin group of antibiotics.<ref>PMID:11137816</ref> <ref>PMID:12240298</ref>
+[https://www.uniprot.org/uniprot/HMO_AMYOR HMO_AMYOR] Catalyzes the oxidation of p-hydroxymandelate to p-hydroxybenzoylformate in the biosynthesis of L-(4-hydroxyphenyl)glycine and L-(3,5-dihydroxyphenyl)glycine, 2 non-proteinogenic amino acids occurring in the vancomycin group of antibiotics.<ref>PMID:11137816</ref> <ref>PMID:12240298</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Though reactive flavin-N5/C4alpha-oxide intermediates can be spectroscopically profiled for some flavin-assisted enzymatic reactions, their exact chemical configurations are hardly visualized. Structural systems biology and stable isotopic labelling techniques were exploited to correct this stereotypical view. Three transition-like complexes, the alpha-ketoacid...N5-FMN(ox) complex (I), the FMN(ox) -N5-aloxyl-C'alpha(-) -C4alpha(+) zwitterion (II), and the FMN-N5-ethenol-N5-C4alpha-epoxide (III), were determined from mandelate oxidase (Hmo) or its mutant Y128F (monooxygenase) crystals soaked with monofluoropyruvate (a product mimic), establishing that N5 of FMN(ox) an alternative reaction center can polarize to an ylide-like mesomer in the active site. In contrast, four distinct flavin-C4alpha-oxide adducts (IV-VII) from Y128F crystals soaked with selected substrates materialize C4alpha of FMN an intrinsic reaction center, witnessing oxidation, Baeyer-Villiger/peroxide-assisted decarboxylation, and epoxidation reactions. In conjunction with stopped-flow kinetics, the multifaceted flavin-dependent reaction continuum is physically dissected at molecular level for the first time.
+Structural and chemical trapping of flavin-oxide intermediates reveals substrate-directed reaction multiplicity.,Lin KH, Lyu SY, Yeh HW, Li YS, Hsu NS, Huang CM, Wang YL, Shih HW, Wang ZC, Wu CJ, Li TL Protein Sci. 2020 Jul;29(7):1655-1666. doi: 10.1002/pro.3879. Epub 2020 May 26. PMID:32362037<ref>PMID:32362037</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6a4h" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 4-hydroxymandelate oxidase]]
+[[Category: Amycolatopsis orientalis]]
 [[Category: Large Structures]]
-[[Category: Li, T L]]
+[[Category: Li TL]]
-[[Category: Lin, K H]]
+[[Category: Lin KH]]
-[[Category: Flavoprotein]]
-[[Category: Fmn-dependent oxidase]]