7jvl - Revision history

OCA at 15:12, 18 October 2023

2023-10-18T15:12:13Z

←Older revision		Revision as of 15:12, 18 October 2023
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	<StructureSection load='7jvl' size='340' side='right'caption='[[7jvl]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='7jvl' size='340' side='right'caption='[[7jvl]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7jvl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aspfu Aspfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JVL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7JVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jvl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_fumigatus_Af293 Aspergillus fumigatus Af293]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JVL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 2.1Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sidA, Afu2g07680 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ornithine_N(5)-monooxygenase_(NAD(P)H) L-ornithine N(5)-monooxygenase (NAD(P)H)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.196 1.14.13.196] </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=7jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jvl OCA], [https://pdbe.org/7jvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jvl RCSB], [https://www.ebi.ac.uk/pdbsum/7jvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jvl 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=7jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jvl OCA], [~~http~~://pdbe.org/7jvl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jvl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jvl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jvl ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SIDA_ASPFU SIDA_ASPFU]] Catalyzes the conversion of L-ornithine to N(5)-hydroxyornithine, the first step in the biosynthesis of all hydroxamate-containing siderophores, such as the secreted triacetylfusarinine C (TAFC) involved in iron uptake and the intracellular iron storage compound desferriferricrocin (DFFC). Highly specific for its substrate, only hydrolyzing l-ornithine. Has preference for NADPH over NADH, NADPH playing a role in stabilization of the C4a-hydroperoxyflavin intermediate. Essential for virulence.<ref>PMID:15504822</ref> <ref>PMID:16113265</ref> <ref>PMID:20614882</ref> <ref>PMID:22465572</ref>	+	[https://www.uniprot.org/uniprot/SIDA_ASPFU SIDA_ASPFU] Catalyzes the conversion of L-ornithine to N(5)-hydroxyornithine, the first step in the biosynthesis of all hydroxamate-containing siderophores, such as the secreted triacetylfusarinine C (TAFC) involved in iron uptake and the intracellular iron storage compound desferriferricrocin (DFFC). Highly specific for its substrate, only hydrolyzing l-ornithine. Has preference for NADPH over NADH, NADPH playing a role in stabilization of the C4a-hydroperoxyflavin intermediate. Essential for virulence.<ref>PMID:15504822</ref> <ref>PMID:16113265</ref> <ref>PMID:20614882</ref> <ref>PMID:22465572</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7jvl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7jvl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aspfu~~]]	+	[[Category: Aspergillus fumigatus Af293]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Campbell~~, A C~~]]	+	[[Category: Campbell AC]]
-	[[Category: Tanner~~, J J]]~~	+	[[Category: Tanner JJ]]
-	~~[[Category: Flavin-containing monooxygenase]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 13:01, 16 December 2020

2020-12-16T13:01:23Z

←Older revision		Revision as of 13:01, 16 December 2020
Line 1:		Line 1:

	==Structure of the M101A variant of the SidA ornithine hydroxylase complexed with NADP and the FAD in the "out" conformation==		==Structure of the M101A variant of the SidA ornithine hydroxylase complexed with NADP and the FAD in the "out" conformation==
-	<StructureSection load='7jvl' size='340' side='right'caption='[[7jvl]]' scene=''>	+	<StructureSection load='7jvl' size='340' side='right'caption='[[7jvl]], [[Resolution\|resolution]] 2.10Å' 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=7JVL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jvl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspfu Aspfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JVL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JVL 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=7jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jvl OCA], [http://pdbe.org/7jvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jvl RCSB], [http://www.ebi.ac.uk/pdbsum/7jvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jvl 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sidA, Afu2g07680 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ornithine_N(5)-monooxygenase_(NAD(P)H) L-ornithine N(5)-monooxygenase (NAD(P)H)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.196 1.14.13.196] </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=7jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jvl OCA], [http://pdbe.org/7jvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jvl RCSB], [http://www.ebi.ac.uk/pdbsum/7jvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jvl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SIDA_ASPFU SIDA_ASPFU]] Catalyzes the conversion of L-ornithine to N(5)-hydroxyornithine, the first step in the biosynthesis of all hydroxamate-containing siderophores, such as the secreted triacetylfusarinine C (TAFC) involved in iron uptake and the intracellular iron storage compound desferriferricrocin (DFFC). Highly specific for its substrate, only hydrolyzing l-ornithine. Has preference for NADPH over NADH, NADPH playing a role in stabilization of the C4a-hydroperoxyflavin intermediate. Essential for virulence.<ref>PMID:15504822</ref> <ref>PMID:16113265</ref> <ref>PMID:20614882</ref> <ref>PMID:22465572</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ornithine hydroxylase known as SidA is a class B flavin monooxygenase that catalyzes the first step in the biosynthesis of hydroxamate-containing siderophores in Aspergillus fumigatus. Crystallographic studies of SidA revealed that the FAD undergoes dramatic conformational changes between out and in states during the catalytic cycle. We sought insight into the origins and purpose of flavin motion in class B monooxygenases by probing the function of Met101, a residue that contacts the pyrimidine ring of the in FAD. Steady-state kinetic measurements showed that the mutant variant M101A has a 25-fold lower turnover number. Pre-steady-state kinetic measurements, pH profiles, and solvent kinetic isotope effect measurements were used to isolate the microscopic step that is responsible for the reduced steady-state activity. The data are consistent with a bottleneck in the final step of the mechanism, which involves flavin dehydration and the release of hydroxy-l-ornithine and NADP(+). Crystal structures were determined for M101A in the resting state and complexed with NADP(+). The resting enzyme structure is similar to that of wild-type SidA, consistent with M101A exhibiting normal kinetics for flavin reduction by NADPH and wild-type affinity for NADPH. In contrast, the structure of the M101A-NADP(+) complex unexpectedly shows the FAD adopting the out conformation and may represent a stalled conformation that is responsible for the slow kinetics. Altogether, our data support a previous proposal that one purpose of the FAD conformational change from in to out in class B flavin monooxygenases is to eject spent NADP(+) in preparation for a new catalytic cycle.
		+
		+	Structural Determinants of Flavin Dynamics in a Class B Monooxygenase.,Campbell AC, Robinson R, Mena-Aguilar D, Sobrado P, Tanner JJ Biochemistry. 2020 Dec 8;59(48):4609-4616. doi: 10.1021/acs.biochem.0c00783. Epub, 2020 Nov 23. PMID:33226785<ref>PMID:33226785</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jvl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspfu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Campbell AC]]	+	[[Category: Campbell, A C]]
-	[[Category: Tanner JJ]]	+	[[Category: Tanner, J J]]
		+	[[Category: Flavin-containing monooxygenase]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Oxidoreductase]]

OCA at 07:55, 2 December 2020

2020-12-02T07:55:56Z

←Older revision		Revision as of 07:55, 2 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7jvl ~~is ON HOLD until Paper Publication~~	+	==Structure of the M101A variant of the SidA ornithine hydroxylase complexed with NADP and the FAD in the "out" conformation==
-		+	<StructureSection load='7jvl' size='340' side='right'caption='[[7jvl]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JVL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JVL FirstGlance]. <br>
-	~~Description~~:	+	</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=7jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jvl OCA], [http://pdbe.org/7jvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jvl RCSB], [http://www.ebi.ac.uk/pdbsum/7jvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jvl ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Campbell AC]]
		+	[[Category: Tanner JJ]]

OCA at 07:01, 16 September 2020

2020-09-16T07:01:59Z

←Older revision		Revision as of 07:01, 16 September 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7jvl is ON HOLD	+	The entry 7jvl is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7jvl" [edit=sysop:move=sysop]

2020-09-02T05:22:24Z

Protected "7jvl" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:22, 2 September 2020

OCA: New page: '''Unreleased structure''' The entry 7jvl is ON HOLD Authors: Description: Category: Unreleased Structures

2020-09-02T05:22:23Z

New page: '''Unreleased structure''' The entry 7jvl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7jvl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]