6n21 - Revision history

OCA at 06:43, 11 October 2023

2023-10-11T06:43:34Z

←Older revision		Revision as of 06:43, 11 October 2023
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	<StructureSection load='6n21' size='340' side='right'caption='[[6n21]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6n21' size='340' side='right'caption='[[6n21]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n21]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Chrysonilia_crassa Chrysonilia~~ crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N21 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n21]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N21 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GE21DRAFT_6499 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=5141 Chrysonilia crassa]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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=6n21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n21 OCA], [~~http~~://pdbe.org/6n21 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n21 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n21 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n21 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=6n21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n21 OCA], [https://pdbe.org/6n21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n21 RCSB], [https://www.ebi.ac.uk/pdbsum/6n21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n21 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0B0DIC8_NEUCS A0A0B0DIC8_NEUCS]
	<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: Chrysonilia crassa]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Khadka, N~~]]	+	[[Category: Neurospora crassa]]
-	[[Category: ~~Kiser, P D~~]]	+	[[Category: Khadka N]]
-	[[Category: ~~Beta-propeller]]~~	+	[[Category: Kiser PD]]
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Non-heme iron protein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 12:36, 17 July 2019

2019-07-17T12:36:58Z

←Older revision		Revision as of 12:36, 17 July 2019
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	<StructureSection load='6n21' size='340' side='right'caption='[[6n21]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6n21' size='340' side='right'caption='[[6n21]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n21]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n21]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chrysonilia_crassa Chrysonilia crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N21 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GE21DRAFT_6499 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5141 Chrysonilia crassa])</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=6n21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n21 OCA], [http://pdbe.org/6n21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n21 RCSB], [http://www.ebi.ac.uk/pdbsum/6n21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n21 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=6n21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n21 OCA], [http://pdbe.org/6n21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n21 RCSB], [http://www.ebi.ac.uk/pdbsum/6n21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n21 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chrysonilia crassa]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Khadka, N]]		[[Category: Khadka, N]]

OCA at 06:16, 12 June 2019

2019-06-12T06:16:58Z

←Older revision		Revision as of 06:16, 12 June 2019
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	<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=6n21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n21 OCA], [http://pdbe.org/6n21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n21 RCSB], [http://www.ebi.ac.uk/pdbsum/6n21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n21 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=6n21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n21 OCA], [http://pdbe.org/6n21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n21 RCSB], [http://www.ebi.ac.uk/pdbsum/6n21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n21 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carotenoid cleavage dioxygenases (CCDs) use a non-heme Fe(II) cofactor to split alkene bonds of carotenoid and stilbenoid substrates. The iron centers of CCDs are typically five-coordinate in their resting states, with solvent occupying an exchangeable site. The involvement of this iron-bound solvent in CCD catalysis has not been experimentally addressed, but computational studies suggest two possible roles: 1) solvent dissociation provides a coordination site for O2, or 2) solvent remains bound to iron but changes its equilibrium position to allow O2 binding and potentially acts as a proton source. To test these predictions, we investigated isotope effects (H2O versus D2O) on two stilbenoid-cleaving CCDs, Novosphingobium aromaticivorans oxygenase 2 (NOV2) and Neurospora crassa carotenoid oxygenase 1 (CAO1), using piceatannol as a substrate. NOV2 exhibited an inverse isotope effect (kH/kD ~0.6) in an air-saturated buffer, suggesting that solvent dissociates from iron during the catalytic cycle. By contrast, CAO1 displayed a normal isotope effect (kH/kD ~1.7) suggesting proton transfer in the rate-limiting step. X-ray absorption spectroscopy on NOV2 and CAO1 indicated that the protonation states of the iron ligands are unchanged within the pH 6.5-8.5 and that the Fe(II)-aquo bond is minimally altered by substrate binding. We pinpointed the origin of the differential kinetic behaviors of NOV2 and CAO1 to a single amino acid difference near the solvent-binding site of iron, and X-ray crystallography revealed that the substitution alters binding of diffusible ligand to the iron center. We conclude that solvent-iron dissociation and proton transfer are both associated with the CCD catalytic mechanism.
		+
		+	Evidence for distinct rate-limiting steps in the cleavage of alkenes by carotenoid cleavage dioxygenases.,Khadka N, Farquhar ER, Hill HE, Shi W, von Lintig J, Kiser PD J Biol Chem. 2019 May 28. pii: RA119.007535. doi: 10.1074/jbc.RA119.007535. PMID:31138651<ref>PMID:31138651</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6n21" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 22:48, 5 June 2019

2019-06-05T22:48:48Z

←Older revision		Revision as of 22:48, 5 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n21 ~~is ON HOLD until Paper Publication~~	+	==Structure of wild-type CAO1==
-		+	<StructureSection load='6n21' size='340' side='right'caption='[[6n21]], [[Resolution\|resolution]] 2.04Å' scene=''>
-	~~Authors~~: ~~Khadka, N~~.~~, Kiser, P~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n21]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N21 FirstGlance]. <br>
-	~~Description~~: ~~Structure of wild~~-~~type CAO1~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6n21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n21 OCA], [http://pdbe.org/6n21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n21 RCSB], [http://www.ebi.ac.uk/pdbsum/6n21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n21 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Kiser~~, P.D]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Khadka, N]]		[[Category: Khadka, N]]
		+	[[Category: Kiser, P D]]
		+	[[Category: Beta-propeller]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Non-heme iron protein]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "6n21" [edit=sysop:move=sysop]

2018-12-02T19:08:29Z

Protected "6n21" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:08, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n21 is ON HOLD until Paper Publication Authors: Khadka, N., Kiser, P.D. Description: Structure of wild-type CAO1 [[Category: Unreleased Structures...

2018-12-02T19:08:28Z

New page: '''Unreleased structure''' The entry 6n21 is ON HOLD until Paper Publication Authors: Khadka, N., Kiser, P.D. Description: Structure of wild-type CAO1 [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 6n21 is ON HOLD until Paper Publication

Authors: Khadka, N., Kiser, P.D.

Description: Structure of wild-type CAO1
[[Category: Unreleased Structures]]
[[Category: Kiser, P.D]]
[[Category: Khadka, N]]