2czu - Revision history

OCA at 08:23, 20 March 2024

2024-03-20T08:23:20Z

←Older revision		Revision as of 08:23, 20 March 2024
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	<StructureSection load='2czu' size='340' side='right'caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2czu' size='340' side='right'caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CZU FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2czt\|2czt]]</div></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~~='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Prostaglandin~~-~~D_synthase Prostaglandin-D synthase]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.~~2 5.~~3.99.2] </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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [https://pdbe.org/2czu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [https://www.ebi.ac.uk/pdbsum/2czu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2czu ProSAT], [https://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [https://pdbe.org/2czu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [https://www.ebi.ac.uk/pdbsum/2czu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2czu ProSAT], [https://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PTGDS_MOUSE PTGDS_MOUSE]] Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophopic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system.<ref>PMID:8922532</ref> <ref>PMID:9892701</ref> <ref>PMID:10781097</ref> <ref>PMID:11751991</ref> <ref>PMID:12077186</ref> <ref>PMID:17715133</ref> <ref>PMID:19546224</ref> <ref>PMID:19833210</ref>	+	[https://www.uniprot.org/uniprot/PTGDS_MOUSE PTGDS_MOUSE] Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophopic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system.<ref>PMID:8922532</ref> <ref>PMID:9892701</ref> <ref>PMID:10781097</ref> <ref>PMID:11751991</ref> <ref>PMID:12077186</ref> <ref>PMID:17715133</ref> <ref>PMID:19546224</ref> <ref>PMID:19833210</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2czu ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2czu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Lipocalin type prostaglandin D synthase (L-PGDS) is a multifunctional protein acting as a somnogen (PGD2)-producing enzyme, an extracellular transporter of various lipophilic ligands, and an amyloid-beta chaperone in human cerebrospinal fluid. In this study, we determined the crystal structures of two different conformers of mouse L-PGDS, one with an open cavity of the beta-barrel and the other with a closed cavity due to the movement of the flexible E-F loop. The upper compartment of the central large cavity contains the catalytically essential Cys65 residue and its network of hydrogen bonds with the polar residues Ser45, Thr67, and Ser81, whereas the lower compartment is composed of hydrophobic amino acid residues that are highly conserved among other lipocalins. SH titration analysis combined with site-directed mutagenesis revealed that the Cys65 residue is activated by its interaction with Ser45 and Thr67 and that the S45A/T67A/S81A mutant showed less than 10% of the L-PGDS activity. The conformational change between the open and closed states of the cavity indicates that the mobile calyx contributes to the multiligand binding ability of L-PGDS.
-
-	Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.,Kumasaka T, Aritake K, Ago H, Irikura D, Tsurumura T, Yamamoto M, Miyano M, Urade Y, Hayaishi O J Biol Chem. 2009 Aug 14;284(33):22344-52. Epub 2009 Jun 22. PMID:19546224<ref>PMID:19546224</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2czu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice]]~~	+	[[Category: Mus musculus]]
-	~~[[Category: Prostaglandin-D synthase~~]]	+	[[Category: Ago H]]
-	[[Category: Ago, H]]	+	[[Category: Aritake K]]
-	[[Category: Aritake, K]]	+	[[Category: Hayaishi O]]
-	[[Category: Hayaishi, O]]	+	[[Category: Inoue T]]
-	[[Category: Inoue, T]]	+	[[Category: Irikura D]]
-	[[Category: Irikura, D]]	+	[[Category: Kumasaka T]]
-	[[Category: Kumasaka, T]]	+	[[Category: Miyano M]]
-	[[Category: Miyano, M]]	+	[[Category: Urade Y]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Yamamoto M]]
-	[[Category: Urade, Y]]	+
-	[[Category: Yamamoto, M]]	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Lipocalin]]~~	+
-	~~[[Category: Lpgds_p212121 native]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 06:47, 10 November 2021

2021-11-10T06:47:41Z

←Older revision		Revision as of 06:47, 10 November 2021
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	<StructureSection load='2czu' size='340' side='right'caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2czu' size='340' side='right'caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2CZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CZU FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2czt\|2czt]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [~~http~~://pdbe.org/2czu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2czu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2czu ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [https://pdbe.org/2czu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [https://www.ebi.ac.uk/pdbsum/2czu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2czu ProSAT], [https://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PTGDS_MOUSE PTGDS_MOUSE]] Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophopic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system.<ref>PMID:8922532</ref> <ref>PMID:9892701</ref> <ref>PMID:10781097</ref> <ref>PMID:11751991</ref> <ref>PMID:12077186</ref> <ref>PMID:17715133</ref> <ref>PMID:19546224</ref> <ref>PMID:19833210</ref>	+	[[https://www.uniprot.org/uniprot/PTGDS_MOUSE PTGDS_MOUSE]] Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophopic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system.<ref>PMID:8922532</ref> <ref>PMID:9892701</ref> <ref>PMID:10781097</ref> <ref>PMID:11751991</ref> <ref>PMID:12077186</ref> <ref>PMID:17715133</ref> <ref>PMID:19546224</ref> <ref>PMID:19833210</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:45, 4 March 2020

2020-03-04T07:45:22Z

←Older revision		Revision as of 07:45, 4 March 2020
Line 1:		Line 1:

	==lipocalin-type prostaglandin D synthase==		==lipocalin-type prostaglandin D synthase==
-	<StructureSection load='2czu' size='340' side='right' caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2czu' size='340' side='right'caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZU FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Prostaglandin-D synthase]]		[[Category: Prostaglandin-D synthase]]

OCA at 06:30, 30 May 2018

2018-05-30T06:30:55Z

←Older revision		Revision as of 06:30, 30 May 2018
Line 1:		Line 1:
		+
	==lipocalin-type prostaglandin D synthase==		==lipocalin-type prostaglandin D synthase==
	<StructureSection load='2czu' size='340' side='right' caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2czu' size='340' side='right' caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [http://pdbe.org/2czu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [http://www.ebi.ac.uk/pdbsum/2czu PDBsum], [http://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [http://pdbe.org/2czu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [http://www.ebi.ac.uk/pdbsum/2czu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2czu ProSAT], [http://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cz/2czu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cz/2czu_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 08:07, 10 February 2016

2016-02-10T08:07:46Z

←Older revision		Revision as of 08:07, 10 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2czu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:58, 11 September 2015

2015-09-11T06:58:38Z

←Older revision		Revision as of 06:58, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2czu' size='340' side='right' caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2czu' size='340' side='right' caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZU FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [http://www.ebi.ac.uk/pdbsum/2czu PDBsum], [http://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [http://pdbe.org/2czu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [http://www.ebi.ac.uk/pdbsum/2czu PDBsum], [http://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 2czu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Prostaglandin-D synthase]]		[[Category: Prostaglandin-D synthase]]
	[[Category: Ago, H]]		[[Category: Ago, H]]

OCA at 12:54, 25 December 2014

2014-12-25T12:54:40Z

←Older revision		Revision as of 12:54, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [http://www.ebi.ac.uk/pdbsum/2czu PDBsum], [http://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</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=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [http://www.ebi.ac.uk/pdbsum/2czu PDBsum], [http://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PTGDS_MOUSE PTGDS_MOUSE]] Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophopic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system.<ref>PMID:8922532</ref> <ref>PMID:9892701</ref> <ref>PMID:10781097</ref> <ref>PMID:11751991</ref> <ref>PMID:12077186</ref> <ref>PMID:17715133</ref> <ref>PMID:19546224</ref> <ref>PMID:19833210</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Prostaglandin-D synthase]]		[[Category: Prostaglandin-D synthase]]
-	[[Category: Ago, H.]]	+	[[Category: Ago, H]]
-	[[Category: Aritake, K.]]	+	[[Category: Aritake, K]]
-	[[Category: Hayaishi, O.]]	+	[[Category: Hayaishi, O]]
-	[[Category: Inoue, T.]]	+	[[Category: Inoue, T]]
-	[[Category: Irikura, D.]]	+	[[Category: Irikura, D]]
-	[[Category: Kumasaka, T.]]	+	[[Category: Kumasaka, T]]
-	[[Category: Miyano, M.]]	+	[[Category: Miyano, M]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Urade, Y.]]	+	[[Category: Urade, Y]]
-	[[Category: Yamamoto, M.]]	+	[[Category: Yamamoto, M]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Lipocalin]]		[[Category: Lipocalin]]
	[[Category: Lpgds_p212121 native]]		[[Category: Lpgds_p212121 native]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 04:04, 29 September 2014

2014-09-29T04:04:32Z

←Older revision		Revision as of 04:04, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2czu.~~png~~\|~~left~~\|200px]]	+	==lipocalin-type prostaglandin D synthase==
		+	<StructureSection load='2czu' size='340' side='right' caption='[[2czu]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2czt\|2czt]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2czu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2czu RCSB], [http://www.ebi.ac.uk/pdbsum/2czu PDBsum], [http://www.topsan.org/Proteins/RSGI/2czu TOPSAN]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cz/2czu_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lipocalin type prostaglandin D synthase (L-PGDS) is a multifunctional protein acting as a somnogen (PGD2)-producing enzyme, an extracellular transporter of various lipophilic ligands, and an amyloid-beta chaperone in human cerebrospinal fluid. In this study, we determined the crystal structures of two different conformers of mouse L-PGDS, one with an open cavity of the beta-barrel and the other with a closed cavity due to the movement of the flexible E-F loop. The upper compartment of the central large cavity contains the catalytically essential Cys65 residue and its network of hydrogen bonds with the polar residues Ser45, Thr67, and Ser81, whereas the lower compartment is composed of hydrophobic amino acid residues that are highly conserved among other lipocalins. SH titration analysis combined with site-directed mutagenesis revealed that the Cys65 residue is activated by its interaction with Ser45 and Thr67 and that the S45A/T67A/S81A mutant showed less than 10% of the L-PGDS activity. The conformational change between the open and closed states of the cavity indicates that the mobile calyx contributes to the multiligand binding ability of L-PGDS.

-	~~{{STRUCTURE_2czu\| PDB=2czu \| SCENE= }}~~	+	Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.,Kumasaka T, Aritake K, Ago H, Irikura D, Tsurumura T, Yamamoto M, Miyano M, Urade Y, Hayaishi O J Biol Chem. 2009 Aug 14;284(33):22344-52. Epub 2009 Jun 22. PMID:19546224<ref>PMID:19546224</ref>

-	~~===lipocalin-type prostaglandin D synthase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19546224}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2czu]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA].~~	+

	==See Also==		==See Also==
	*[[Prostaglandin D synthase\|Prostaglandin D synthase]]		*[[Prostaglandin D synthase\|Prostaglandin D synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019546224<~~/~~ref~~><~~ref group="xtra">PMID:012761195</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Prostaglandin-D synthase]]		[[Category: Prostaglandin-D synthase]]

OCA at 16:55, 20 October 2012

2012-10-20T16:55:02Z

←Older revision		Revision as of 16:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2czu]] is a 2 chain structure ~~of [[Prostaglandin D synthase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA].	+	[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA].

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019546224</ref><ref group="xtra">PMID:012761195~~</ref><ref group="xtra">PMID:009892701~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019546224</ref><ref group="xtra">PMID:012761195</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Prostaglandin-D synthase]]		[[Category: Prostaglandin-D synthase]]

OCA at 23:14, 26 July 2012

2012-07-26T23:14:21Z

←Older revision		Revision as of 23:14, 26 July 2012
Line 1:		Line 1:
	[[Image:2czu.png\|left\|200px]]		[[Image:2czu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2czu", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2czu\| PDB=2czu \| SCENE= }}		{{STRUCTURE_2czu\| PDB=2czu \| SCENE= }}

	===lipocalin-type prostaglandin D synthase===		===lipocalin-type prostaglandin D synthase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19546224}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19546224 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19546224}}		{{ABSTRACT_PUBMED_19546224}}

	==About this Structure==		==About this Structure==
-	[[2czu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA].	+	[[2czu]] is a 2 chain structure of [[Prostaglandin D synthase]] with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZU OCA].
		+
		+	==See Also==
		+	*[[Prostaglandin D synthase\|Prostaglandin D synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19546224~~</ref><ref group="xtra">PMID:~~12761195~~</ref><ref group="xtra">PMID:~~9892701~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019546224</ref><ref group="xtra">PMID:012761195</ref><ref group="xtra">PMID:009892701</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Prostaglandin-D synthase]]		[[Category: Prostaglandin-D synthase]]