7olo - Revision history

OCA at 12:52, 1 February 2024

OCA — Thu, 01 Feb 2024 12:52:19 GMT

←Older revision		Revision as of 12:52, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7olo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans_FGSC_A4 Aspergillus nidulans FGSC A4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLO FirstGlance]. <br>		<table><tr><td colspan='2'>[[7olo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans_FGSC_A4 Aspergillus nidulans FGSC A4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO0:(3~{Z})-4-methyl-3-(phenylmethylidene)-1~{H}-1,4-benzodiazepine-2,5-dione'>CO0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO0:(3~{Z})-4-methyl-3-(phenylmethylidene)-1~{H}-1,4-benzodiazepine-2,5-dione'>CO0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=7olo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olo OCA], [https://pdbe.org/7olo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olo RCSB], [https://www.ebi.ac.uk/pdbsum/7olo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olo 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=7olo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olo OCA], [https://pdbe.org/7olo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olo RCSB], [https://www.ebi.ac.uk/pdbsum/7olo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ASQJ_EMENI ASQJ_EMENI]] Iron/alpha-ketoglutarate-dependent dioxygenase; part of the gene cluster that mediates the biosynthesis of the aspoquinolone mycotoxins (PubMed:25251934, PubMed:26553478). The first stage is catalyzed by the nonribosomal pepdide synthetase asqK that condenses anthranilic acid and O-methyl-L-tyrosine to produce 4'-methoxycyclopeptin (PubMed:25251934). AsqK is also able to use anthranilic acid and L-phenylalanine as substrates to produce cyclopeptin, but at a tenfold lower rate (PubMed:25251934). 4'-methoxycyclopeptin is then converted to 4'-methoxydehydrocyclopeptin by the ketoglutarate-dependent dioxygenase asqJ through dehydrogenation to form a double bond between C-alpha and C-beta of the O-methyltyrosine side chain (PubMed:25251934, PubMed:26553478). AsqJ also converts its first product 4'-methoxydehydrocyclopeptin to 4'-methoxycyclopenin (PubMed:25251934). AsqJ is a very unique dioxygenase which is capable of catalyzing radical-mediated dehydrogenation and epoxidation reactions sequentially on a 6,7-benzo-diazepinedione substrate in the 4'-methoxyviridicatin biosynthetic pathway (PubMed:25251934). The following conversion of 4'-methoxycyclopenin into 4'-methoxyviridicatin proceeds non-enzymatically (PubMed:25251934). AsqJ is also capable of converting cyclopeptin into dehydrocyclopeptin and cyclopenin in a sequential fashion (PubMed:25251934). Cyclopenin can be converted into viridicatin non-enzymatically (PubMed:25251934). 4'-methoxyviridicatin likely acts as a precursor of quinolone natural products, such as aspoquinolones, peniprequinolones, penigequinolones, and yaequinolones (PubMed:25251934). Further characterization of the remaining genes in the cluster has still to be done to determine the exact identity of quinolone products this cluster is responsible for biosynthesizing (PubMed:25251934).<ref>PMID:25251934</ref> <ref>PMID:26553478</ref>	+	[https://www.uniprot.org/uniprot/ASQJ_EMENI ASQJ_EMENI] Iron/alpha-ketoglutarate-dependent dioxygenase; part of the gene cluster that mediates the biosynthesis of the aspoquinolone mycotoxins (PubMed:25251934, PubMed:26553478). The first stage is catalyzed by the nonribosomal pepdide synthetase asqK that condenses anthranilic acid and O-methyl-L-tyrosine to produce 4'-methoxycyclopeptin (PubMed:25251934). AsqK is also able to use anthranilic acid and L-phenylalanine as substrates to produce cyclopeptin, but at a tenfold lower rate (PubMed:25251934). 4'-methoxycyclopeptin is then converted to 4'-methoxydehydrocyclopeptin by the ketoglutarate-dependent dioxygenase asqJ through dehydrogenation to form a double bond between C-alpha and C-beta of the O-methyltyrosine side chain (PubMed:25251934, PubMed:26553478). AsqJ also converts its first product 4'-methoxydehydrocyclopeptin to 4'-methoxycyclopenin (PubMed:25251934). AsqJ is a very unique dioxygenase which is capable of catalyzing radical-mediated dehydrogenation and epoxidation reactions sequentially on a 6,7-benzo-diazepinedione substrate in the 4'-methoxyviridicatin biosynthetic pathway (PubMed:25251934). The following conversion of 4'-methoxycyclopenin into 4'-methoxyviridicatin proceeds non-enzymatically (PubMed:25251934). AsqJ is also capable of converting cyclopeptin into dehydrocyclopeptin and cyclopenin in a sequential fashion (PubMed:25251934). Cyclopenin can be converted into viridicatin non-enzymatically (PubMed:25251934). 4'-methoxyviridicatin likely acts as a precursor of quinolone natural products, such as aspoquinolones, peniprequinolones, penigequinolones, and yaequinolones (PubMed:25251934). Further characterization of the remaining genes in the cluster has still to be done to determine the exact identity of quinolone products this cluster is responsible for biosynthesizing (PubMed:25251934).<ref>PMID:25251934</ref> <ref>PMID:26553478</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7olo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7olo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:45, 7 September 2022

OCA — Wed, 07 Sep 2022 19:45:33 GMT

←Older revision		Revision as of 19:45, 7 September 2022
Line 1:		Line 1:

	==Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol==		==Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol==
-	<StructureSection load='7olo' size='340' side='right'caption='[[7olo]]' scene=''>	+	<StructureSection load='7olo' size='340' side='right'caption='[[7olo]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7olo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans_FGSC_A4 Aspergillus nidulans FGSC A4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLO FirstGlance]. <br>
-	</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=7olo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olo OCA], [https://pdbe.org/7olo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olo RCSB], [https://www.ebi.ac.uk/pdbsum/7olo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olo ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO0:(3~{Z})-4-methyl-3-(phenylmethylidene)-1~{H}-1,4-benzodiazepine-2,5-dione'>CO0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=7olo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olo OCA], [https://pdbe.org/7olo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olo RCSB], [https://www.ebi.ac.uk/pdbsum/7olo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/ASQJ_EMENI ASQJ_EMENI]] Iron/alpha-ketoglutarate-dependent dioxygenase; part of the gene cluster that mediates the biosynthesis of the aspoquinolone mycotoxins (PubMed:25251934, PubMed:26553478). The first stage is catalyzed by the nonribosomal pepdide synthetase asqK that condenses anthranilic acid and O-methyl-L-tyrosine to produce 4'-methoxycyclopeptin (PubMed:25251934). AsqK is also able to use anthranilic acid and L-phenylalanine as substrates to produce cyclopeptin, but at a tenfold lower rate (PubMed:25251934). 4'-methoxycyclopeptin is then converted to 4'-methoxydehydrocyclopeptin by the ketoglutarate-dependent dioxygenase asqJ through dehydrogenation to form a double bond between C-alpha and C-beta of the O-methyltyrosine side chain (PubMed:25251934, PubMed:26553478). AsqJ also converts its first product 4'-methoxydehydrocyclopeptin to 4'-methoxycyclopenin (PubMed:25251934). AsqJ is a very unique dioxygenase which is capable of catalyzing radical-mediated dehydrogenation and epoxidation reactions sequentially on a 6,7-benzo-diazepinedione substrate in the 4'-methoxyviridicatin biosynthetic pathway (PubMed:25251934). The following conversion of 4'-methoxycyclopenin into 4'-methoxyviridicatin proceeds non-enzymatically (PubMed:25251934). AsqJ is also capable of converting cyclopeptin into dehydrocyclopeptin and cyclopenin in a sequential fashion (PubMed:25251934). Cyclopenin can be converted into viridicatin non-enzymatically (PubMed:25251934). 4'-methoxyviridicatin likely acts as a precursor of quinolone natural products, such as aspoquinolones, peniprequinolones, penigequinolones, and yaequinolones (PubMed:25251934). Further characterization of the remaining genes in the cluster has still to be done to determine the exact identity of quinolone products this cluster is responsible for biosynthesizing (PubMed:25251934).<ref>PMID:25251934</ref> <ref>PMID:26553478</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dioxygenases catalyze stereoselective oxygen atom transfer in metabolic pathways of biological, industrial, and pharmaceutical importance, but their precise chemical principles remain controversial. The alpha-ketoglutarate (alphaKG)-dependent dioxygenase AsqJ synthesizes biomedically active quinolone alkaloids via desaturation and subsequent epoxidation of a carbon-carbon bond in the cyclopeptin substrate. Here, we combine high-resolution X-ray crystallography with enzyme engineering, quantum-classical (QM/MM) simulations, and biochemical assays to describe a peroxidic intermediate that bridges the substrate and active site metal ion in AsqJ. Homolytic cleavage of this moiety during substrate epoxidation generates an activated high-valent ferryl (Fe(IV) = O) species that mediates the next catalytic cycle, possibly without the consumption of the metabolically valuable alphaKG cosubstrate. Our combined findings provide an important understanding of chemical bond activation principles in complex enzymatic reaction networks and molecular mechanisms of dioxygenases.
		+
		+	Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ.,Auman D, Ecker F, Mader SL, Dorst KM, Brauer A, Widmalm G, Groll M, Kaila VRI J Am Chem Soc. 2022 Aug 18. doi: 10.1021/jacs.2c05650. PMID:35980821<ref>PMID:35980821</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7olo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus nidulans FGSC A4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Auman D]]		[[Category: Auman D]]

OCA at 06:42, 31 August 2022

OCA — Wed, 31 Aug 2022 06:42:43 GMT

←Older revision		Revision as of 06:42, 31 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7olo ~~is ON HOLD until Paper Publication~~	+	==Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol==
-		+	<StructureSection load='7olo' size='340' side='right'caption='[[7olo]]' scene=''>
-	~~Authors~~: ~~Auman, D~~.~~, Mader, S~~.L.~~, Ecker, F~~.~~, Dorst, K~~.~~, Braeuer, A~~., ~~Widmalm, G~~., ~~Groll~~, M., ~~Kaila, V~~.R.I.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLO FirstGlance]. <br>
-	~~Description: Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol~~	+	</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=7olo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olo OCA], [https://pdbe.org/7olo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olo RCSB], [https://www.ebi.ac.uk/pdbsum/7olo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olo ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Auman, D]]	+	__TOC__
-	[[Category: ~~Dorst, K~~]]	+	</StructureSection>
-	[[Category: ~~Groll, M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kaila, V.R.I~~]]	+	[[Category: Auman D]]
-	[[Category: ~~Braeuer, A~~]]	+	[[Category: Braeuer A]]
-	[[Category: ~~Widmalm, G~~]]	+	[[Category: Dorst K]]
-	[[Category: Mader~~, S.L~~]]	+	[[Category: Ecker F]]
-	[[Category: ~~Ecker, F~~]]	+	[[Category: Groll M]]
		+	[[Category: Kaila VRI]]
		+	[[Category: Mader SL]]
		+	[[Category: Widmalm G]]

OCA at 13:37, 2 June 2021

OCA — Wed, 02 Jun 2021 13:37:19 GMT

←Older revision		Revision as of 13:37, 2 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7olo is ON HOLD	+	The entry 7olo is ON HOLD until Paper Publication

	Authors: Auman, D., Mader, S.L., Ecker, F., Dorst, K., Braeuer, A., Widmalm, G., Groll, M., Kaila, V.R.I.		Authors: Auman, D., Mader, S.L., Ecker, F., Dorst, K., Braeuer, A., Widmalm, G., Groll, M., Kaila, V.R.I.
Line 7:		Line 7:
	Description: Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol		Description: Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kaila, V.R.I]]
-	[[Category: Widmalm, G]]
	[[Category: Auman, D]]		[[Category: Auman, D]]
	[[Category: Dorst, K]]		[[Category: Dorst, K]]
	[[Category: Groll, M]]		[[Category: Groll, M]]
		+	[[Category: Kaila, V.R.I]]
	[[Category: Braeuer, A]]		[[Category: Braeuer, A]]
		+	[[Category: Widmalm, G]]
	[[Category: Mader, S.L]]		[[Category: Mader, S.L]]
	[[Category: Ecker, F]]		[[Category: Ecker, F]]

OCA: Protected "7olo" [edit=sysop:move=sysop]

OCA — Wed, 26 May 2021 08:11:52 GMT

Protected "7olo" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:11, 26 May 2021

OCA: New page: '''Unreleased structure''' The entry 7olo is ON HOLD Authors: Auman, D., Mader, S.L., Ecker, F., Dorst, K., Braeuer, A., Widmalm, G., Groll, M., Kaila, V.R.I. Description: Dioxygenase ...

OCA — Wed, 26 May 2021 08:11:51 GMT

New page: '''Unreleased structure''' The entry 7olo is ON HOLD Authors: Auman, D., Mader, S.L., Ecker, F., Dorst, K., Braeuer, A., Widmalm, G., Groll, M., Kaila, V.R.I. Description: Dioxygenase ...

New page

'''Unreleased structure'''

The entry 7olo is ON HOLD

Authors: Auman, D., Mader, S.L., Ecker, F., Dorst, K., Braeuer, A., Widmalm, G., Groll, M., Kaila, V.R.I.

Description: Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol
[[Category: Unreleased Structures]]
[[Category: Kaila, V.R.I]]
[[Category: Widmalm, G]]
[[Category: Auman, D]]
[[Category: Dorst, K]]
[[Category: Groll, M]]
[[Category: Braeuer, A]]
[[Category: Mader, S.L]]
[[Category: Ecker, F]]