5zm3 - Revision history

OCA at 09:00, 22 November 2023

OCA — Wed, 22 Nov 2023 09:00:36 GMT

←Older revision		Revision as of 09:00, 22 November 2023
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	==Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B==		==Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B==
-	<StructureSection load='5zm3' size='340' side='right' caption='[[5zm3]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='5zm3' size='340' side='right'caption='[[5zm3]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zm3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_16819 Atcc 16819~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZM3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zm3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_stellatus Aspergillus stellatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZM3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9FR:(6aS,8aR,12aS,12bR,13aR)-5,6a,9,9,12a,13a-hexamethyl-7,8,8a,9,11,12,12a,12b,13,13a-decahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1H,6aH)-trione'>9FR</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]] 2.25Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">andA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1549217 ATCC 16819])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9FR:(6aS,8aR,12aS,12bR,13aR)-5,6a,9,9,12a,13a-hexamethyl-7,8,8a,9,11,12,12a,12b,13,13a-decahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1H,6aH)-trione'>9FR</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=5zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm3 OCA], [~~http~~://pdbe.org/5zm3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zm3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zm3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm3 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=5zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm3 OCA], [https://pdbe.org/5zm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zm3 RCSB], [https://www.ebi.ac.uk/pdbsum/5zm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ANDA_EMEVA ANDA_EMEVA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5zm3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zm3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 16819~~]]	+	[[Category: Aspergillus stellatus]]
-	[[Category: ~~Nakashima, Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Senda, T~~]]	+	[[Category: Nakashima Y]]
-	[[Category: ~~Oxidoreductase]]~~	+	[[Category: Senda T]]
-	~~[[Category: Oxygenase~~]]	+

OCA at 07:53, 29 August 2018

OCA — Wed, 29 Aug 2018 07:53:42 GMT

←Older revision		Revision as of 07:53, 29 August 2018
Line 3:		Line 3:
	<StructureSection load='5zm3' size='340' side='right' caption='[[5zm3]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='5zm3' size='340' side='right' caption='[[5zm3]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zm3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zm3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_16819 Atcc 16819]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZM3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9FR:(6aS,8aR,12aS,12bR,13aR)-5,6a,9,9,12a,13a-hexamethyl-7,8,8a,9,11,12,12a,12b,13,13a-decahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1H,6aH)-trione'>9FR</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=9FR:(6aS,8aR,12aS,12bR,13aR)-5,6a,9,9,12a,13a-hexamethyl-7,8,8a,9,11,12,12a,12b,13,13a-decahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1H,6aH)-trione'>9FR</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">andA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1549217 ATCC 16819])</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=5zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm3 OCA], [http://pdbe.org/5zm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zm3 RCSB], [http://www.ebi.ac.uk/pdbsum/5zm3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm3 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=5zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm3 OCA], [http://pdbe.org/5zm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zm3 RCSB], [http://www.ebi.ac.uk/pdbsum/5zm3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm3 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 16819]]
	[[Category: Nakashima, Y]]		[[Category: Nakashima, Y]]
	[[Category: Senda, T]]		[[Category: Senda, T]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Oxygenase]]		[[Category: Oxygenase]]

OCA at 07:32, 18 July 2018

OCA — Wed, 18 Jul 2018 07:32:21 GMT

←Older revision		Revision as of 07:32, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zm3 is ~~ON HOLD until Apr 01 2020~~	+	==Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B==
		+	<StructureSection load='5zm3' size='340' side='right' caption='[[5zm3]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zm3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZM3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9FR:(6aS,8aR,12aS,12bR,13aR)-5,6a,9,9,12a,13a-hexamethyl-7,8,8a,9,11,12,12a,12b,13,13a-decahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1H,6aH)-trione'>9FR</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=5zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm3 OCA], [http://pdbe.org/5zm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zm3 RCSB], [http://www.ebi.ac.uk/pdbsum/5zm3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm3 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AndA, an Fe(II)/alpha-ketoglutarate (alphaKG)-dependent enzyme, is the key enzyme that constructs the unique and congested bridged-ring system of anditomin (1), by catalyzing consecutive dehydrogenation and isomerization reactions. Although we previously characterized AndA to some extent, the means by which the enzyme facilitates this drastic structural reconstruction have remained elusive. In this study, we have solved three X-ray crystal structures of AndA, in its apo form and in the complexes with Fe(II), alphaKG, and two substrates. The crystal structures and mutational experiments identified several key amino acid residues important for the catalysis and provided insight into how AndA controls the reaction. Furthermore, computational calculations validated the proposed reaction mechanism for the bridged-ring formation and also revealed the requirement of a series of conformational changes during the transformation.

-	~~Authors:~~ Nakashima, Y., Senda, T.	+	Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis.,Nakashima Y, Mitsuhashi T, Matsuda Y, Senda M, Sato H, Yamazaki M, Uchiyama M, Senda T, Abe I J Am Chem Soc. 2018 Jul 4. doi: 10.1021/jacs.8b06084. PMID:29972643<ref>PMID:29972643</ref>

-	~~Description: Fe(II)~~/~~(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Senda, T]]~~	+	<div class="pdbe-citations 5zm3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Nakashima, Y]]		[[Category: Nakashima, Y]]
		+	[[Category: Senda, T]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxygenase]]

OCA at 03:49, 25 April 2018

OCA — Wed, 25 Apr 2018 03:49:38 GMT

←Older revision		Revision as of 03:49, 25 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zm3 is ON HOLD	+	The entry 5zm3 is ON HOLD until Apr 01 2020

	Authors: Nakashima, Y., Senda, T.		Authors: Nakashima, Y., Senda, T.

OCA at 04:03, 18 April 2018

OCA — Wed, 18 Apr 2018 04:03:15 GMT

←Older revision		Revision as of 04:03, 18 April 2018
Line 5:		Line 5:
	Authors: Nakashima, Y., Senda, T.		Authors: Nakashima, Y., Senda, T.

-	Description: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B.	+	Description: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Senda, T]]		[[Category: Senda, T]]
	[[Category: Nakashima, Y]]		[[Category: Nakashima, Y]]

OCA: Protected "5zm3" [edit=sysop:move=sysop]

OCA — Wed, 11 Apr 2018 12:20:18 GMT

Protected "5zm3" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:20, 11 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zm3 is ON HOLD Authors: Nakashima, Y., Senda, T. Description: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B. [[Categor...

OCA — Wed, 11 Apr 2018 12:20:16 GMT

New page: '''Unreleased structure''' The entry 5zm3 is ON HOLD Authors: Nakashima, Y., Senda, T. Description: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B. [[Categor...

New page

'''Unreleased structure'''

The entry 5zm3 is ON HOLD

Authors: Nakashima, Y., Senda, T.

Description: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B.
[[Category: Unreleased Structures]]
[[Category: Senda, T]]
[[Category: Nakashima, Y]]