6a1p: Difference between revisions
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<StructureSection load='6a1p' size='340' side='right'caption='[[6a1p]], [[Resolution|resolution]] 1.51Å' scene=''> | <StructureSection load='6a1p' size='340' side='right'caption='[[6a1p]], [[Resolution|resolution]] 1.51Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6a1p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A1P OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6a1p]] 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=6A1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A1P FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O9:1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol'>9O9</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPY:3-PHENYLPYRUVIC+ACID'>PPY</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]] 1.51Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9O9:1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol'>9O9</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPY:3-PHENYLPYRUVIC+ACID'>PPY</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=6a1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a1p OCA], [https://pdbe.org/6a1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a1p RCSB], [https://www.ebi.ac.uk/pdbsum/6a1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a1p 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 == | |||
The Y128F single mutant of p-hydroxymandelate oxidase (Hmo) is capable of oxidizing mandelate to benzoate via a four-electron oxidative decarboxylation reaction. When benzoylformate (the product of the first two-electron oxidation) and hydrogen peroxide (an oxidant) were used as substrates the reaction did not proceed, suggesting that free hydrogen peroxide is not the committed oxidant in the second two-electron oxidation. How the flavin mononucleotide (FMN)-dependent four-electron oxidation reaction takes place remains elusive. Structural and biochemical explorations have shed new light on this issue. 15 high-resolution crystal structures of Hmo and its mutants liganded with or without a substrate reveal that oxidized FMN (FMNox) possesses a previously unknown electrophilic/nucleophilic duality. In the Y128F mutant the active-site perturbation ensemble facilitates the polarization of FMNox to a nucleophilic ylide, which is in a position to act on an alpha-ketoacid, forming an N5-acyl-FMNred dead-end adduct. In four-electron oxidation, an intramolecular disproportionation reaction via an N5-alkanol-FMNred C'alpha carbanion intermediate may account for the ThDP/PLP/NADPH-independent oxidative decarboxylation reaction. A synthetic 5-deaza-FMNox cofactor in combination with an alpha-hydroxyamide or alpha-ketoamide biochemically and structurally supports the proposed mechanism. | |||
The flavin mononucleotide cofactor in alpha-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level.,Lyu SY, Lin KH, Yeh HW, Li YS, Huang CM, Wang YL, Shih HW, Hsu NS, Wu CJ, Li TL Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):918-929. doi:, 10.1107/S2059798319011938. Epub 2019 Sep 24. PMID:31588923<ref>PMID:31588923</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6a1p" 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]] | ||