5y7t - Revision history

OCA at 10:21, 27 March 2024

OCA — Wed, 27 Mar 2024 10:21:58 GMT

←Older revision		Revision as of 10:21, 27 March 2024
Line 1:		Line 1:

	==Quaternary complex of AsqJ-Fe3+-2OG-D-cyclopeptin==		==Quaternary complex of AsqJ-Fe3+-2OG-D-cyclopeptin==
-	<StructureSection load='5y7t' size='340' side='right' caption='[[5y7t]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5y7t' size='340' side='right'caption='[[5y7t]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y7t]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aspergillus_nidulans~~ Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y7T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y7t]] 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=5Y7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y7T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8R0:(3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione'>8R0</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 2.05Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asqJ, AN9227 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227321 Aspergillus nidulans])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8R0:(3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione'>8R0</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=5y7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7t OCA], [~~http~~://pdbe.org/5y7t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y7t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y7t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7t 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=5y7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7t OCA], [https://pdbe.org/5y7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y7t RCSB], [https://www.ebi.ac.uk/pdbsum/5y7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	AsqJ, an iron(II)- and 2-oxoglutarate-dependent enzyme found in viridicatin-type alkaloid biosynthetic pathways, catalyzes sequential desaturation and epoxidation to produce cyclopenins. Crystal structures of AsqJ bound to cyclopeptin and its C3 epimer are reported. Meanwhile, a detailed mechanistic study was carried out to decipher the desaturation mechanism. These findings suggest that a pathway involving hydrogen atom abstraction at the C10 position of the substrate by a short-lived Fe(IV) -oxo species and the subsequent formation of a carbocation or a hydroxylated intermediate is preferred during AsqJ-catalyzed desaturation.	+

-	Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation.,Liao HJ, Li J, Huang JL, Davidson M, Kurnikov I, Lin TS, Lee JL, Kurnikova M, Guo Y, Chan NL, Chang WC Angew Chem Int Ed Engl. 2018 Jan 3. doi: 10.1002/anie.201710567. PMID:29314482<ref>PMID:29314482</ref>	+	==See Also==
-		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5y7t" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aspergillus nidulans]]	+	[[Category: Aspergillus nidulans FGSC A4]]
-	[[Category: ~~Liao, H J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~D-cyclopeptin]]~~	+	[[Category: Liao HJ]]
-	~~[[Category: Ferric]]~~	+
-	~~[[Category: Initial step]]~~	+
-	~~[[Category: Octahedron]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:47, 7 February 2018

OCA — Wed, 07 Feb 2018 06:47:02 GMT

←Older revision		Revision as of 06:47, 7 February 2018
Line 3:		Line 3:
	<StructureSection load='5y7t' size='340' side='right' caption='[[5y7t]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5y7t' size='340' side='right' caption='[[5y7t]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y7t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y7T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y7t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y7T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8R0:(3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione'>8R0</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8R0:(3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione'>8R0</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">asqJ, AN9227 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227321 Aspergillus nidulans])</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=5y7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7t OCA], [http://pdbe.org/5y7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y7t RCSB], [http://www.ebi.ac.uk/pdbsum/5y7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7t ProSAT]</span></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=5y7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7t OCA], [http://pdbe.org/5y7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y7t RCSB], [http://www.ebi.ac.uk/pdbsum/5y7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7t ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus nidulans]]
	[[Category: Liao, H J]]		[[Category: Liao, H J]]
	[[Category: D-cyclopeptin]]		[[Category: D-cyclopeptin]]

OCA at 18:28, 24 January 2018

OCA — Wed, 24 Jan 2018 18:28:01 GMT

←Older revision		Revision as of 18:28, 24 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y7t is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Quaternary complex of AsqJ-Fe3+-2OG-D-cyclopeptin==
		+	<StructureSection load='5y7t' size='340' side='right' caption='[[5y7t]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y7t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y7T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8R0:(3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione'>8R0</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=5y7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7t OCA], [http://pdbe.org/5y7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y7t RCSB], [http://www.ebi.ac.uk/pdbsum/5y7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7t ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	AsqJ, an iron(II)- and 2-oxoglutarate-dependent enzyme found in viridicatin-type alkaloid biosynthetic pathways, catalyzes sequential desaturation and epoxidation to produce cyclopenins. Crystal structures of AsqJ bound to cyclopeptin and its C3 epimer are reported. Meanwhile, a detailed mechanistic study was carried out to decipher the desaturation mechanism. These findings suggest that a pathway involving hydrogen atom abstraction at the C10 position of the substrate by a short-lived Fe(IV) -oxo species and the subsequent formation of a carbocation or a hydroxylated intermediate is preferred during AsqJ-catalyzed desaturation.

-	~~Authors~~:	+	Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation.,Liao HJ, Li J, Huang JL, Davidson M, Kurnikov I, Lin TS, Lee JL, Kurnikova M, Guo Y, Chan NL, Chang WC Angew Chem Int Ed Engl. 2018 Jan 3. doi: 10.1002/anie.201710567. PMID:29314482<ref>PMID:29314482</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5y7t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Liao, H J]]
		+	[[Category: D-cyclopeptin]]
		+	[[Category: Ferric]]
		+	[[Category: Initial step]]
		+	[[Category: Octahedron]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5y7t" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:14:38 GMT

Protected "5y7t" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:14, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y7t is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:14:37 GMT

New page: '''Unreleased structure''' The entry 5y7t is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y7t is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]