6vi6 - Revision history

OCA at 08:13, 11 October 2023

2023-10-11T08:13:09Z

←Older revision		Revision as of 08:13, 11 October 2023
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	<StructureSection load='6vi6' size='340' side='right'caption='[[6vi6]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6vi6' size='340' side='right'caption='[[6vi6]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cupmc Cupmc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VI6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_metallidurans_CH34 Cupriavidus metallidurans CH34]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VI6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3HA:3-HYDROXYANTHRANILIC+ACID'>3HA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.901Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaC, Rmet_5193 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 CUPMC])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3HA:3-HYDROXYANTHRANILIC+ACID'>3HA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxyanthranilate_3,4-dioxygenase 3-hydroxyanthranilate 3,4-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.6 1.13.11.6] </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=6vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vi6 OCA], [https://pdbe.org/6vi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vi6 RCSB], [https://www.ebi.ac.uk/pdbsum/6vi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vi6 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=6vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vi6 OCA], [https://pdbe.org/6vi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vi6 RCSB], [https://www.ebi.ac.uk/pdbsum/6vi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vi6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/3HAO_CUPMC 3HAO_CUPMC]] Catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde, which spontaneously cyclizes to quinolinate.[HAMAP-Rule:MF_00825]<ref>PMID:15909977</ref>	+	[https://www.uniprot.org/uniprot/3HAO_CUPMC 3HAO_CUPMC] Catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde, which spontaneously cyclizes to quinolinate.[HAMAP-Rule:MF_00825]<ref>PMID:15909977</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~3-hydroxyanthranilate 3,4-dioxygenase]]~~	+	[[Category: Cupriavidus metallidurans CH34]]
-	~~[[Category: Cupmc~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liu, A]]	+	[[Category: Liu A]]
-	[[Category: Liu, F]]	+	[[Category: Liu F]]
-	[[Category: Wang, Y]]	+	[[Category: Wang Y]]
-	[[Category: Yang, Y]]	+	[[Category: Yang Y]]
-	~~[[Category: Extradiol dioxygenase]]~~	+
-	~~[[Category: In crystallo reaction]]~~	+
-	~~[[Category: Intermediate]]~~	+
-	~~[[Category: Nad+ biosynthesis]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 05:47, 6 October 2021

2021-10-06T05:47:16Z

←Older revision		Revision as of 05:47, 6 October 2021
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	==Observing a ring-cleaving dioxygenase in action through a crystalline lens - a substrate monodentately bound structure==		==Observing a ring-cleaving dioxygenase in action through a crystalline lens - a substrate monodentately bound structure==
-	<StructureSection load='6vi6' size='340' side='right'caption='[[6vi6]]' scene=''>	+	<StructureSection load='6vi6' size='340' side='right'caption='[[6vi6]], [[Resolution\|resolution]] 1.90Å' 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=6VI6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VI6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupmc Cupmc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VI6 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vi6 OCA], [~~http~~://pdbe.org/6vi6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vi6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vi6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vi6 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=3HA:3-HYDROXYANTHRANILIC+ACID'>3HA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaC, Rmet_5193 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 CUPMC])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxyanthranilate_3,4-dioxygenase 3-hydroxyanthranilate 3,4-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.6 1.13.11.6] </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=6vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vi6 OCA], [https://pdbe.org/6vi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vi6 RCSB], [https://www.ebi.ac.uk/pdbsum/6vi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vi6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/3HAO_CUPMC 3HAO_CUPMC]] Catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde, which spontaneously cyclizes to quinolinate.[HAMAP-Rule:MF_00825]<ref>PMID:15909977</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-A resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-A resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.
		+
		+	Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens.,Wang Y, Liu KF, Yang Y, Davis I, Liu A Proc Natl Acad Sci U S A. 2020 Jul 30. pii: 2005327117. doi:, 10.1073/pnas.2005327117. PMID:32732435<ref>PMID:32732435</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vi6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 3-hydroxyanthranilate 3,4-dioxygenase]]
		+	[[Category: Cupmc]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liu A]]	+	[[Category: Liu, A]]
-	[[Category: Liu F]]	+	[[Category: Liu, F]]
-	[[Category: Wang Y]]	+	[[Category: Wang, Y]]
-	[[Category: Yang Y]]	+	[[Category: Yang, Y]]
		+	[[Category: Extradiol dioxygenase]]
		+	[[Category: In crystallo reaction]]
		+	[[Category: Intermediate]]
		+	[[Category: Nad+ biosynthesis]]
		+	[[Category: Oxidoreductase]]

OCA at 11:09, 29 July 2020

2020-07-29T11:09:32Z

←Older revision		Revision as of 11:09, 29 July 2020
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-	'''Unreleased structure'''

-	~~The entry 6vi6 is ON HOLD until Paper Publication~~	+	==Observing a ring-cleaving dioxygenase in action through a crystalline lens - a substrate monodentately bound structure==
-		+	<StructureSection load='6vi6' size='340' side='right'caption='[[6vi6]]' scene=''>
-	~~Authors: Wang, Y., Liu, F., Yang, Y., Liu, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VI6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VI6 FirstGlance]. <br>
-	~~Description:~~ Observing a ring-cleaving dioxygenase in action through a crystalline lens -a substrate monodentately bound structure	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vi6 OCA], [http://pdbe.org/6vi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vi6 RCSB], [http://www.ebi.ac.uk/pdbsum/6vi6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vi6 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Liu~~, F~~]]	+	__TOC__
-	[[Category: ~~Yang, Y~~]]	+	</StructureSection>
-	[[Category: Wang, Y]]	+	[[Category: Large Structures]]
-	[[Category: ~~Liu, A~~]]	+	[[Category: Liu A]]
		+	[[Category: Liu F]]
		+	[[Category: Wang Y]]
		+	[[Category: Yang Y]]

OCA at 02:39, 13 February 2020

2020-02-13T02:39:48Z

←Older revision		Revision as of 02:39, 13 February 2020
Line 5:		Line 5:
	Authors: Wang, Y., Liu, F., Yang, Y., Liu, A.		Authors: Wang, Y., Liu, F., Yang, Y., Liu, A.

-	Description: ~~Probing Extradiol Dioxygenase Mechanism~~ in ~~NAD+ Biosynthesis by Viewing Reaction Cycle Intermediates~~-a substrate monodentately bound structure	+	Description: Observing a ring-cleaving dioxygenase in action through a crystalline lens -a substrate monodentately bound structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Liu, F]]
	[[Category: Yang, Y]]		[[Category: Yang, Y]]
	[[Category: Wang, Y]]		[[Category: Wang, Y]]
	[[Category: Liu, A]]		[[Category: Liu, A]]
-	[[Category: Liu, F]]

OCA: Protected "6vi6" [edit=sysop:move=sysop]

2020-01-22T14:30:42Z

Protected "6vi6" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:30, 22 January 2020

OCA: New page: '''Unreleased structure''' The entry 6vi6 is ON HOLD until Paper Publication Authors: Wang, Y., Liu, F., Yang, Y., Liu, A. Description: Probing Extradiol Dioxygenase Mechanism in NAD+ ...

2020-01-22T14:30:40Z

New page: '''Unreleased structure''' The entry 6vi6 is ON HOLD until Paper Publication Authors: Wang, Y., Liu, F., Yang, Y., Liu, A. Description: Probing Extradiol Dioxygenase Mechanism in NAD+ ...

New page

'''Unreleased structure'''

The entry 6vi6 is ON HOLD until Paper Publication

Authors: Wang, Y., Liu, F., Yang, Y., Liu, A.

Description: Probing Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Reaction Cycle Intermediates-a substrate monodentately bound structure
[[Category: Unreleased Structures]]
[[Category: Yang, Y]]
[[Category: Wang, Y]]
[[Category: Liu, A]]
[[Category: Liu, F]]