This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2rq0

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:29, 12 September 2018

Solution Structure of Mouse Lipocalin-type Prostaglandin D Synthase Possessing the Intrinsic Disulfide Bond

Structural highlights

2rq0 is a 1 chain structure with sequence from Lk3 transgenic mice. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	Ptgds (LK3 transgenic mice)
Activity:	Prostaglandin-D synthase, with EC number 5.3.99.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Lipocalin-type prostaglandin D synthase (L-PGDS) acts as both a PGD(2) synthase and an extracellular transporter for small lipophilic molecules. From a series of biochemical studies, it has been found that L-PGDS has an ability to bind a variety of lipophilic ligands such as biliverdin, bilirubin and retinoids in vitro. Therefore, we considered that it is necessary to clarify the molecular structure of L-PGDS upon binding ligand in order to understand the physiological relevance of L-PGDS as a transporter protein. We investigated a molecular structure of L-PGDS/biliverdin complex by small-angle X-ray scattering (SAXS) and multi-dimensional NMR measurements, and characterized the binding mechanism in detail. SAXS measurements revealed that L-PGDS has a globular shape and becomes compact by 1.3A in radius of gyration on binding biliverdin. NMR experiments revealed that L-PGDS possessed an eight-stranded antiparallel beta-barrel forming a central cavity. Upon the titration with biliverdin, some cross-peaks for residues surrounding the cavity and EF-loop and H2-helix above the beta-barrel shifted, and the intensity of other cross-peaks decreased with signal broadenings in (1)H-(15)N heteronuclear single quantum coherence spectra. These results demonstrate that L-PGDS holds biliverdin within the beta-barrel, and the conformation of the loop regions above the beta-barrel changes upon binding biliverdin. Through such a conformational change, the whole molecule of L-PGDS becomes compact.

Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR.,Miyamoto Y, Nishimura S, Inoue K, Shimamoto S, Yoshida T, Fukuhara A, Yamada M, Urade Y, Yagi N, Ohkubo T, Inui T J Struct Biol. 2010 Feb;169(2):209-18. Epub 2009 Oct 13. PMID:19833210^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hoffmann A, Bachner D, Betat N, Lauber J, Gross G. Developmental expression of murine Beta-trace in embryos and adult animals suggests a function in maturation and maintenance of blood-tissue barriers. Dev Dyn. 1996 Nov;207(3):332-43. PMID:8922532 doi:<332::AID-AJA10>3.0.CO;2-6 http://dx.doi.org/10.1002/(SICI)1097-0177(199611)207:3<332::AID-AJA10>3.0.CO;2-6
↑ Eguchi N, Minami T, Shirafuji N, Kanaoka Y, Tanaka T, Nagata A, Yoshida N, Urade Y, Ito S, Hayaishi O. Lack of tactile pain (allodynia) in lipocalin-type prostaglandin D synthase-deficient mice. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):726-30. PMID:9892701
↑ Pinzar E, Kanaoka Y, Inui T, Eguchi N, Urade Y, Hayaishi O. Prostaglandin D synthase gene is involved in the regulation of non-rapid eye movement sleep. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4903-7. PMID:10781097 doi:http://dx.doi.org/10.1073/pnas.090093997
↑ Fujitani Y, Kanaoka Y, Aritake K, Uodome N, Okazaki-Hatake K, Urade Y. Pronounced eosinophilic lung inflammation and Th2 cytokine release in human lipocalin-type prostaglandin D synthase transgenic mice. J Immunol. 2002 Jan 1;168(1):443-9. PMID:11751991
↑ Taniike M, Mohri I, Eguchi N, Beuckmann CT, Suzuki K, Urade Y. Perineuronal oligodendrocytes protect against neuronal apoptosis through the production of lipocalin-type prostaglandin D synthase in a genetic demyelinating model. J Neurosci. 2002 Jun 15;22(12):4885-96. PMID:12077186
↑ Shimamoto S, Yoshida T, Inui T, Gohda K, Kobayashi Y, Fujimori K, Tsurumura T, Aritake K, Urade Y, Ohkubo T. NMR solution structure of lipocalin-type prostaglandin D synthase: evidence for partial overlapping of catalytic pocket and retinoic acid-binding pocket within the central cavity. J Biol Chem. 2007 Oct 26;282(43):31373-9. Epub 2007 Aug 22. PMID:17715133 doi:10.1074/jbc.M700123200
↑ Kumasaka T, Aritake K, Ago H, Irikura D, Tsurumura T, Yamamoto M, Miyano M, Urade Y, Hayaishi O. Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase. J Biol Chem. 2009 Aug 14;284(33):22344-52. Epub 2009 Jun 22. PMID:19546224 doi:10.1074/jbc.M109.018341
↑ Miyamoto Y, Nishimura S, Inoue K, Shimamoto S, Yoshida T, Fukuhara A, Yamada M, Urade Y, Yagi N, Ohkubo T, Inui T. Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR. J Struct Biol. 2010 Feb;169(2):209-18. Epub 2009 Oct 13. PMID:19833210 doi:10.1016/j.jsb.2009.10.005
↑ Miyamoto Y, Nishimura S, Inoue K, Shimamoto S, Yoshida T, Fukuhara A, Yamada M, Urade Y, Yagi N, Ohkubo T, Inui T. Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR. J Struct Biol. 2010 Feb;169(2):209-18. Epub 2009 Oct 13. PMID:19833210 doi:10.1016/j.jsb.2009.10.005

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2rq0"

@@ Line 1: / Line 1: @@
 ==Solution Structure of Mouse Lipocalin-type Prostaglandin D Synthase Possessing the Intrinsic Disulfide Bond==
 <StructureSection load='2rq0' size='340' side='right' caption='[[2rq0]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ptgds ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=2rq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rq0 OCA], [http://pdbe.org/2rq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2rq0 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=2rq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rq0 OCA], [http://pdbe.org/2rq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2rq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rq0 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rq/2rq0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rq/2rq0_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 41: / Line 42: @@
 [[Category: Nishimura, S]]
 [[Category: Beta-barrel]]
+[[Category: Cytoplasm]]
 [[Category: Endoplasmic reticulum]]
 [[Category: Fatty acid biosynthesis]]

2rq0

From Proteopedia

Revision as of 08:29, 12 September 2018

Solution Structure of Mouse Lipocalin-type Prostaglandin D Synthase Possessing the Intrinsic Disulfide Bond

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox