6a3d
From Proteopedia
(Difference between revisions)
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<StructureSection load='6a3d' size='340' side='right'caption='[[6a3d]], [[Resolution|resolution]] 1.92Å' scene=''> | <StructureSection load='6a3d' size='340' side='right'caption='[[6a3d]], [[Resolution|resolution]] 1.92Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6a3d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A3D OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[6a3d]] 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=6A3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A3D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9PX:1-deoxy-1-[(4aS)-4a-[(methoxycarbonyl)peroxy]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol'>9PX</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.923Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9PX:1-deoxy-1-[(4aS)-4a-[(methoxycarbonyl)peroxy]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol'>9PX</scene></td></tr> | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6a3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a3d OCA], [https://pdbe.org/6a3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a3d RCSB], [https://www.ebi.ac.uk/pdbsum/6a3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a3d ProSAT]</span></td></tr> |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [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> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6a3d" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Amycolatopsis orientalis]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Li | + | [[Category: Li TL]] |
| - | [[Category: Lin | + | [[Category: Lin KH]] |
| - | + | ||
| - | + | ||
Current revision
The crystal structure of Mandelate oxidase Y128F with 4-Br-2-hydroxy-methylphenylacetate
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