5m98 - Revision history

OCA at 18:32, 1 November 2023

2023-11-01T18:32:13Z

←Older revision		Revision as of 18:32, 1 November 2023
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	<StructureSection load='5m98' size='340' side='right'caption='[[5m98]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5m98' size='340' side='right'caption='[[5m98]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m98]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M98 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5M98 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m98]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M98 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M98 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>uox ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=7955 Brachidanio rerio])</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]] 2.8Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase~~]~~, with EC number [http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=5m98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m98 OCA], [https://pdbe.org/5m98 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m98 RCSB], [https://www.ebi.ac.uk/pdbsum/5m98 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m98 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=5m98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m98 OCA], [~~http~~://pdbe.org/5m98 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m98 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m98 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m98 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~Q6DG85_DANRE Q6DG85_DANRE]~~] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.[PIRNR:PIRNR000241]	+	[https://www.uniprot.org/uniprot/URIC_DANRE URIC_DANRE] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.[PIRNR:PIRNR000241][RuleBase:RU004455]<ref>PMID:27922051</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Urate ~~Oxidase~~\|Urate ~~Oxidase~~]]	+	*[[Urate oxidase 3D structures\|Urate oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	~~[[Category: Factor independent urate hydroxylase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berni, R]]	+	[[Category: Berni R]]
-	[[Category: Cendron, l]]	+	[[Category: Cendron l]]
-	[[Category: Percudani, R]]	+	[[Category: Percudani R]]
-	[[Category: Zanotti, G]]	+	[[Category: Zanotti G]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Purine metabolism]]~~	+
-	~~[[Category: Urate]]~~	+
-	~~[[Category: Uric acid]]~~	+
-	~~[[Category: Uricolytic activity~~]]	+

OCA at 07:12, 19 August 2020

2020-08-19T07:12:22Z

←Older revision		Revision as of 07:12, 19 August 2020
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	==Crystal structure of urate oxidase from zebrafish==		==Crystal structure of urate oxidase from zebrafish==
-	<StructureSection load='5m98' size='340' side='right' caption='[[5m98]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5m98' size='340' side='right'caption='[[5m98]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m98]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M98 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M98 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m98]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M98 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M98 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uox ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=5m98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m98 OCA], [http://pdbe.org/5m98 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m98 RCSB], [http://www.ebi.ac.uk/pdbsum/5m98 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m98 ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=5m98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m98 OCA], [http://pdbe.org/5m98 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m98 RCSB], [http://www.ebi.ac.uk/pdbsum/5m98 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m98 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5m98" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5m98" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Urate Oxidase\|Urate Oxidase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Factor independent urate hydroxylase]]		[[Category: Factor independent urate hydroxylase]]
		+	[[Category: Large Structures]]
	[[Category: Berni, R]]		[[Category: Berni, R]]
	[[Category: Cendron, l]]		[[Category: Cendron, l]]

OCA at 21:24, 22 December 2016

2016-12-22T21:24:41Z

←Older revision		Revision as of 21:24, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5m98 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of urate oxidase from zebrafish==
		+	<StructureSection load='5m98' size='340' side='right' caption='[[5m98]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5m98]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M98 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M98 FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=5m98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m98 OCA], [http://pdbe.org/5m98 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m98 RCSB], [http://www.ebi.ac.uk/pdbsum/5m98 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m98 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q6DG85_DANRE Q6DG85_DANRE]] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.[PIRNR:PIRNR000241]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Urate oxidase (Uox) catalyses the first reaction of oxidative uricolysis, a three-step enzymatic pathway that allows some animals to eliminate purine nitrogen through a water-soluble compound. Inactivation of the pathway in hominoids leads to elevated levels of sparingly soluble urate and puts humans at risk of hyperuricemia and gout. The uricolytic activities lost during evolution can be replaced by enzyme therapy. Here we report on the functional and structural characterization of Uox from zebrafish and the effects on the enzyme of the missense mutation (F216S) that preceded Uox pseudogenization in hominoids. Using a kinetic assay based on the enzymatic suppression of the spectroscopic interference of the Uox reaction product, we found that the F216S mutant has the same turnover number of the wild-type enzyme but a much-reduced affinity for the urate substrate and xanthine inhibitor. Our results indicate that the last functioning Uox in hominoid evolution had an increased Michaelis constant, possibly near to upper end of the normal range of urate in the human serum (~300 muM). Changes in the renal handling of urate during primate evolution can explain the genetic modification of uricolytic activities in the hominoid lineage without the need of assuming fixation of deleterious mutations.

-	~~Authors: Zanotti, G~~., ~~Cendron~~, l., ~~Percudani~~, R., Berni, R.	+	Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids.,Marchetti M, Liuzzi A, Fermi B, Corsini R, Folli C, Speranzini V, Gandolfi F, Bettati S, Ronda L, Cendron L, Berni R, Zanotti G, Percudani R Sci Rep. 2016 Dec 6;6:38302. doi: 10.1038/srep38302. PMID:27922051<ref>PMID:27922051</ref>

-	~~Description: Crystal structure~~ of ~~urate oxidase from zebrafish~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5m98" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Factor independent urate hydroxylase]]
	[[Category: Berni, R]]		[[Category: Berni, R]]
-	[[Category: Cendron, ~~L]]~~	+	[[Category: Cendron, l]]
-	~~[[Category: Zanotti, G~~]]	+
	[[Category: Percudani, R]]		[[Category: Percudani, R]]
		+	[[Category: Zanotti, G]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Purine metabolism]]
		+	[[Category: Urate]]
		+	[[Category: Uric acid]]
		+	[[Category: Uricolytic activity]]

OCA: Protected "5m98" [edit=sysop:move=sysop]

2016-12-09T16:31:04Z

Protected "5m98" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:31, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5m98 is ON HOLD until Paper Publication Authors: Zanotti, G., Cendron, l., Percudani, R., Berni, R. Description: Crystal structure of urate oxidase...

2016-12-09T16:31:02Z

New page: '''Unreleased structure''' The entry 5m98 is ON HOLD until Paper Publication Authors: Zanotti, G., Cendron, l., Percudani, R., Berni, R. Description: Crystal structure of urate oxidase...

New page

'''Unreleased structure'''

The entry 5m98 is ON HOLD until Paper Publication

Authors: Zanotti, G., Cendron, l., Percudani, R., Berni, R.

Description: Crystal structure of urate oxidase from zebrafish
[[Category: Unreleased Structures]]
[[Category: Berni, R]]
[[Category: Cendron, L]]
[[Category: Zanotti, G]]
[[Category: Percudani, R]]