4c7z - Revision history

OCA at 12:05, 20 December 2023

2023-12-20T12:05:42Z

←Older revision		Revision as of 12:05, 20 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4c7z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C7Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[4c7z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C7Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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]] 1.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [https://pdbe.org/4c7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [https://www.ebi.ac.uk/pdbsum/4c7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c7z 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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [https://pdbe.org/4c7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [https://www.ebi.ac.uk/pdbsum/4c7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c7z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MOP_MEGGA MOP_MEGGA]]	+	[https://www.uniprot.org/uniprot/MOP_MEGGA MOP_MEGGA]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mononuclear Mo-containing enzymes of the xanthine oxidase (XO) family catalyze the oxidative hydroxylation of aldehydes and heterocyclic compounds. The molybdenum active site shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. The XO family member aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is an exception as presents in its catalytically competent form an equatorial oxo ligand instead of the sulfido ligand. Despite this structural difference, inactive samples of DgAOR can be activated upon incubation with dithionite plus sulfide, a procedure similar to that used for activation of desulfo-XO. The fact that DgAOR does not need a sulfido ligand for catalysis indicates that the process leading to the activation of inactive DgAOR samples is different to that of desulfo-XO. We now report a combined kinetic and X-ray crystallographic study to unveil the enzyme modification responsible for the inactivation and the chemistry that occurs at the Mo site when DgAOR is activated. In contrast to XO, which is activated by resulfuration of the Mo site, DgAOR activation/inactivation is governed by the oxidation state of the dithiolene moiety of the pyranopterin cofactor, which demonstrates the non-innocent behavior of the pyranopterin in enzyme activity. We also showed that DgAOR incubation with dithionite plus sulfide in the presence of dioxygen produces hydrogen peroxide not associated with the enzyme activation. The peroxide molecule coordinates to molybdenum in a eta(2) fashion inhibiting the enzyme activity.
		+
		+	Kinetic and Structural Studies of Aldehyde Oxidoreductase from Desulfovibrio gigas Reveal a Dithiolene-Based Chemistry for Enzyme Activation and Inhibition by H2O2.,Marangon J, Correia HD, Brondino CD, Moura JJ, Romao MJ, Gonzalez PJ, Santos-Silva T PLoS One. 2013 Dec 31;8(12):e83234. doi: 10.1371/journal.pone.0083234. PMID:24391748<ref>PMID:24391748</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4c7z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:31, 7 September 2022

2022-09-07T17:31:31Z

←Older revision		Revision as of 17:31, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='4c7z' size='340' side='right'caption='[[4c7z]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='4c7z' size='340' side='right'caption='[[4c7z]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4c7z]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Desulfovibrio_gigas Desulfovibrio~~ gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=4C7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4c7z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C7Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [https://pdbe.org/4c7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [https://www.ebi.ac.uk/pdbsum/4c7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c7z ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c7y\|4c7y]], [[4c80\|4c80]]</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(FAD-independent) Aldehyde dehydrogenase (FAD-independent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.7 1.2.99.7] </span></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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [~~http~~://pdbe.org/4c7z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4c7z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4c7z ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/MOP_MEGGA MOP_MEGGA]]
-	Mononuclear Mo-containing enzymes of the xanthine oxidase (XO) family catalyze the oxidative hydroxylation of aldehydes and heterocyclic compounds. The molybdenum active site shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. The XO family member aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is an exception as presents in its catalytically competent form an equatorial oxo ligand instead of the sulfido ligand. Despite this structural difference, inactive samples of DgAOR can be activated upon incubation with dithionite plus sulfide, a procedure similar to that used for activation of desulfo-XO. The fact that DgAOR does not need a sulfido ligand for catalysis indicates that the process leading to the activation of inactive DgAOR samples is different to that of desulfo-XO. We now report a combined kinetic and X-ray crystallographic study to unveil the enzyme modification responsible for the inactivation and the chemistry that occurs at the Mo site when DgAOR is activated. In contrast to XO, which is activated by resulfuration of the Mo site, DgAOR activation/inactivation is governed by the oxidation state of the dithiolene moiety of the pyranopterin cofactor, which demonstrates the non-innocent behavior of the pyranopterin in enzyme activity. We also showed that DgAOR incubation with dithionite plus sulfide in the presence of dioxygen produces hydrogen peroxide not associated with the enzyme activation. The peroxide molecule coordinates to molybdenum in a eta(2) fashion inhibiting the enzyme activity.	+
-		+
-	Kinetic and Structural Studies of Aldehyde Oxidoreductase from Desulfovibrio gigas Reveal a Dithiolene-Based Chemistry for Enzyme Activation and Inhibition by H2O2.,Marangon J, Correia HD, Brondino CD, Moura JJ, Romao MJ, Gonzalez PJ, Santos-Silva T PLoS One. 2013 Dec 31;8(12):~~e83234. doi: 10.1371~~/~~journal.pone.0083234. PMID:24391748<ref>PMID:24391748<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 4c7z" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Desulfovibrio gigas]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Correia, H D~~]]	+	[[Category: Megalodesulfovibrio gigas]]
-	[[Category: ~~Romao, M J~~]]	+	[[Category: Correia HD]]
-	[[Category: ~~Santos-Silva, T~~]]	+	[[Category: Romao MJ]]
-	[[Category: ~~Activation]]~~	+	[[Category: Santos-Silva T]]
-	~~[[Category: Inactivation]]~~	+
-	~~[[Category: Molybdenum enzyme]]~~	+
-	~~[[Category: Mop]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:17, 4 November 2020

2020-11-04T08:17:07Z

←Older revision		Revision as of 08:17, 4 November 2020
Line 1:		Line 1:

	==Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide==		==Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide==
-	<StructureSection load='4c7z' size='340' side='right' caption='[[4c7z]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='4c7z' size='340' side='right'caption='[[4c7z]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4c7z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4C7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4c7z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4C7Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c7y\|4c7y]], [[4c80\|4c80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c7y\|4c7y]], [[4c80\|4c80]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(FAD-independent) Aldehyde dehydrogenase (FAD-independent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.7 1.2.99.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(FAD-independent) Aldehyde dehydrogenase (FAD-independent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.7 1.2.99.7] </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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [http://pdbe.org/4c7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [http://www.ebi.ac.uk/pdbsum/4c7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4c7z ProSAT]</span></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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [http://pdbe.org/4c7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [http://www.ebi.ac.uk/pdbsum/4c7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4c7z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio gigas]]		[[Category: Desulfovibrio gigas]]
		+	[[Category: Large Structures]]
	[[Category: Correia, H D]]		[[Category: Correia, H D]]
	[[Category: Romao, M J]]		[[Category: Romao, M J]]

OCA at 11:28, 11 August 2016

2016-08-11T11:28:53Z

←Older revision		Revision as of 11:28, 11 August 2016
Line 1:		Line 1:
		+
	==Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide==		==Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide==
	<StructureSection load='4c7z' size='340' side='right' caption='[[4c7z]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='4c7z' size='340' side='right' caption='[[4c7z]], [[Resolution\|resolution]] 1.55Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c7y\|4c7y]], [[4c80\|4c80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c7y\|4c7y]], [[4c80\|4c80]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(FAD-independent) Aldehyde dehydrogenase (FAD-independent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.7 1.2.99.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(FAD-independent) Aldehyde dehydrogenase (FAD-independent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.7 1.2.99.7] </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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [http://www.ebi.ac.uk/pdbsum/4c7z PDBsum]</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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [http://pdbe.org/4c7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [http://www.ebi.ac.uk/pdbsum/4c7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4c7z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4c7z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:47, 20 January 2015

2015-01-20T08:47:58Z

←Older revision		Revision as of 08:47, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4c7z\| PDB=4c7z \| SCENE= }}~~	+	==Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide==
-	===Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide===	+	<StructureSection load='4c7z' size='340' side='right' caption='[[4c7z]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24391748}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4c7z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C7Z FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c7y\|4c7y]], [[4c80\|4c80]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(FAD-independent) Aldehyde dehydrogenase (FAD-independent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.7 1.2.99.7] </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=4c7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4c7z RCSB], [http://www.ebi.ac.uk/pdbsum/4c7z PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mononuclear Mo-containing enzymes of the xanthine oxidase (XO) family catalyze the oxidative hydroxylation of aldehydes and heterocyclic compounds. The molybdenum active site shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. The XO family member aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is an exception as presents in its catalytically competent form an equatorial oxo ligand instead of the sulfido ligand. Despite this structural difference, inactive samples of DgAOR can be activated upon incubation with dithionite plus sulfide, a procedure similar to that used for activation of desulfo-XO. The fact that DgAOR does not need a sulfido ligand for catalysis indicates that the process leading to the activation of inactive DgAOR samples is different to that of desulfo-XO. We now report a combined kinetic and X-ray crystallographic study to unveil the enzyme modification responsible for the inactivation and the chemistry that occurs at the Mo site when DgAOR is activated. In contrast to XO, which is activated by resulfuration of the Mo site, DgAOR activation/inactivation is governed by the oxidation state of the dithiolene moiety of the pyranopterin cofactor, which demonstrates the non-innocent behavior of the pyranopterin in enzyme activity. We also showed that DgAOR incubation with dithionite plus sulfide in the presence of dioxygen produces hydrogen peroxide not associated with the enzyme activation. The peroxide molecule coordinates to molybdenum in a eta(2) fashion inhibiting the enzyme activity.

-	~~==About this Structure==~~	+	Kinetic and Structural Studies of Aldehyde Oxidoreductase from Desulfovibrio gigas Reveal a Dithiolene-Based Chemistry for Enzyme Activation and Inhibition by H2O2.,Marangon J, Correia HD, Brondino CD, Moura JJ, Romao MJ, Gonzalez PJ, Santos-Silva T PLoS One. 2013 Dec 31;8(12):e83234. doi: 10.1371/journal.pone.0083234. PMID:24391748<ref>PMID:24391748</ref>
-	~~[[4c7z]] is a 1 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Desulfovibrio_gigas~~ Desulfovibrio gigas]. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4C7Z OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024391748</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Desulfovibrio gigas]]		[[Category: Desulfovibrio gigas]]
-	[[Category: Correia, H D.]]	+	[[Category: Correia, H D]]
-	[[Category: Romao, M J.]]	+	[[Category: Romao, M J]]
-	[[Category: Santos-Silva, T.]]	+	[[Category: Santos-Silva, T]]
	[[Category: Activation]]		[[Category: Activation]]
	[[Category: Inactivation]]		[[Category: Inactivation]]

OCA at 08:17, 15 January 2014

2014-01-15T08:17:44Z

←Older revision		Revision as of 08:17, 15 January 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4c7z\| PDB=4c7z \| SCENE= }}
		+	===Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide===
		+	{{ABSTRACT_PUBMED_24391748}}

-	~~The entry~~ 4c7z is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4c7z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C7Z OCA].

-	~~Authors~~: Correia, H.D., Romao, M.J., Santos-Silva, T.	+	==Reference==
-		+	<ref group="xtra">PMID:024391748</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Aldehyde~~ Oxidoreductase ~~from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide~~	+	[[Category: Desulfovibrio gigas]]
		+	[[Category: Correia, H D.]]
		+	[[Category: Romao, M J.]]
		+	[[Category: Santos-Silva, T.]]
		+	[[Category: Activation]]
		+	[[Category: Inactivation]]
		+	[[Category: Molybdenum enzyme]]
		+	[[Category: Mop]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "4c7z" [edit=sysop:move=sysop]

2013-10-10T05:27:23Z

Protected "4c7z" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:27, 10 October 2013

OCA: New page: '''Unreleased structure''' The entry 4c7z is ON HOLD until Paper Publication Authors: Correia, H.D., Romao, M.J., Santos-Silva, T. Description: Aldehyde Oxidoreductase from Desulfovibr...

2013-10-10T05:27:22Z

New page: '''Unreleased structure''' The entry 4c7z is ON HOLD until Paper Publication Authors: Correia, H.D., Romao, M.J., Santos-Silva, T. Description: Aldehyde Oxidoreductase from Desulfovibr...

New page

'''Unreleased structure'''

The entry 4c7z is ON HOLD until Paper Publication

Authors: Correia, H.D., Romao, M.J., Santos-Silva, T.

Description: Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide