6a4g - Revision history

OCA at 09:18, 22 November 2023

OCA — Wed, 22 Nov 2023 09:18:03 GMT

←Older revision		Revision as of 09:18, 22 November 2023
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	<StructureSection load='6a4g' size='340' side='right'caption='[[6a4g]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6a4g' size='340' side='right'caption='[[6a4g]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a4g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A4G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a4g]] 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=6A4G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A4G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Q6:1-deoxy-1-[(4aS)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol'>9Q6</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]] 2.04Å</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=9Q6:1-deoxy-1-[(4aS)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol'>9Q6</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=6a4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4g OCA], [~~http~~://pdbe.org/6a4g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a4g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a4g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4g 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=6a4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4g OCA], [https://pdbe.org/6a4g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a4g RCSB], [https://www.ebi.ac.uk/pdbsum/6a4g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6a4g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~4-hydroxymandelate oxidase~~]]	+	[[Category: Amycolatopsis orientalis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li~~, T L~~]]	+	[[Category: Li TL]]
-	[[Category: Lin~~, K H]]~~	+	[[Category: Lin KH]]
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Fmn-dependent oxidase~~]]	+

OCA at 05:49, 19 June 2019

OCA — Wed, 19 Jun 2019 05:49:49 GMT

←Older revision		Revision as of 05:49, 19 June 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6a4g is ~~ON HOLD until Paper Publication~~	+	==Mandelate oxidase mutant-Y128F with the monooxide FMN adduct==
-		+	<StructureSection load='6a4g' size='340' side='right'caption='[[6a4g]], [[Resolution\|resolution]] 2.04Å' scene=''>
-	~~Authors~~: Li, T.L., ~~Lin~~, K.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6a4g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A4G FirstGlance]. <br>
-	~~Description~~: ~~Mandelate oxidase mutant~~-~~Y128F with~~ the ~~monooxide FMN adduct~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Q6:1-deoxy-1-[(4aS)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol'>9Q6</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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>
-	[[Category: Li, T.L]]	+	<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=6a4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4g OCA], [http://pdbe.org/6a4g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a4g RCSB], [http://www.ebi.ac.uk/pdbsum/6a4g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4g ProSAT]</span></td></tr>
-	[[Category: Lin, K.H]]	+	</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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 4-hydroxymandelate oxidase]]
		+	[[Category: Large Structures]]
		+	[[Category: Li, T L]]
		+	[[Category: Lin, K H]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Fmn-dependent oxidase]]

OCA at 03:55, 11 July 2018

OCA — Wed, 11 Jul 2018 03:55:00 GMT

←Older revision		Revision as of 03:55, 11 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6a4g is ON HOLD	+	The entry 6a4g is ON HOLD until Paper Publication

	Authors: Li, T.L., Lin, K.H.		Authors: Li, T.L., Lin, K.H.

OCA: Protected "6a4g" [edit=sysop:move=sysop]

OCA — Wed, 27 Jun 2018 03:53:43 GMT

Protected "6a4g" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:53, 27 June 2018

OCA: New page: '''Unreleased structure''' The entry 6a4g is ON HOLD Authors: Li, T.L., Lin, K.H. Description: Mandelate oxidase mutant-Y128F with the monooxide FMN adduct [[Category: Unreleased Struc...

OCA — Wed, 27 Jun 2018 03:53:42 GMT

New page: '''Unreleased structure''' The entry 6a4g is ON HOLD Authors: Li, T.L., Lin, K.H. Description: Mandelate oxidase mutant-Y128F with the monooxide FMN adduct [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 6a4g is ON HOLD

Authors: Li, T.L., Lin, K.H.

Description: Mandelate oxidase mutant-Y128F with the monooxide FMN adduct
[[Category: Unreleased Structures]]
[[Category: Li, T.L]]
[[Category: Lin, K.H]]