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2dm6

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[[Image:2dm6.png|left|200px]]
 
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{{STRUCTURE_2dm6| PDB=2dm6 | SCENE= }}
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==Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex==
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<StructureSection load='2dm6' size='340' side='right'caption='[[2dm6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2dm6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cavpo Cavpo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DM6 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMN:INDOMETHACIN'>IMN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1v3v|1v3v]], [[1v3t|1v3t]], [[1v3u|1v3u]]</div></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dm6 OCA], [https://pdbe.org/2dm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dm6 RCSB], [https://www.ebi.ac.uk/pdbsum/2dm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dm6 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dm6 TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/PTGR1_CAVPO PTGR1_CAVPO]] Functions as 15-oxo-prostaglandin 13-reductase and acts on 15-oxo-PGE1, 15-oxo-PGE2 and 15-oxo-PGE2-alpha. Catalyzes the conversion of leukotriene B4 into its biologically less active metabolite, 12-oxo-leukotriene B4. This is an initial and key step of metabolic inactivation of leukotriene B4.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/2dm6_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2dm6 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of the ternary complex of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin (15-oxo-PG) 13-reductase (LTB4 12HD/PGR), an essential enzyme for eicosanoid inactivation pathways, with indomethacin and NADP+ has been solved. An indomethacin molecule bound in the anti-configuration at one of the two active site clefts of the homo-dimer interface in the LTB4 12HD/PGR and was confirmed by a binding calorimetry. The chlorobenzene ring is buried in the hydrophobic pore used as a binding site by the omega-chain of 15-oxo-PGE2. The carboxyl group interacts with the guanidino group of Arg56 and the phenolic hydroxyl group of Tyr262. Indomethacin shows a broad spectrum of efficacy against lipid-mediator related proteins including cyclooxygenase-2, phospholipase A2, PGF synthase and PGE synthase-2 but in the syn-configuration as well as LTB4 12HD/PGR in the anti-configuration. Indomethacin does not necessarily mimic the binding mode of the lipid-mediator substrates in the active sites of these complex structures. Thus, the broad spectrum of indomethacin efficacy can be attributed to its ability to adopt a range of different stable conformations. This allows the indomethacin to adapt to the distinct binding site features of each protein whilst maintaining favorable interactions between the carboxyl group and a counter charged functional group.
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===Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex===
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Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex reveals the structural basis of broad spectrum indomethacin efficacy.,Hori T, Ishijima J, Yokomizo T, Ago H, Shimizu T, Miyano M J Biochem. 2006 Sep;140(3):457-66. Epub 2006 Aug 17. PMID:16916844<ref>PMID:16916844</ref>
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{{ABSTRACT_PUBMED_16916844}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 2dm6" style="background-color:#fffaf0;"></div>
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[[2dm6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cavia_porcellus Cavia porcellus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DM6 OCA].
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==See Also==
==See Also==
*[[Leukotriene B4 hydroxydehydrogenase|Leukotriene B4 hydroxydehydrogenase]]
*[[Leukotriene B4 hydroxydehydrogenase|Leukotriene B4 hydroxydehydrogenase]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:016916844</ref><references group="xtra"/>
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__TOC__
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[[Category: Cavia porcellus]]
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</StructureSection>
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[[Category: Ago, H.]]
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[[Category: Cavpo]]
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[[Category: Hori, T.]]
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[[Category: Large Structures]]
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[[Category: Ishijima, J.]]
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[[Category: Ago, H]]
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[[Category: Miyano, M.]]
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[[Category: Hori, T]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Ishijima, J]]
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[[Category: Shimizu, T.]]
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[[Category: Miyano, M]]
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[[Category: Yokomizo, T.]]
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[[Category: Structural genomic]]
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[[Category: Shimizu, T]]
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[[Category: Yokomizo, T]]
[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
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[[Category: Riken structural genomics/proteomics initiative]]
 
[[Category: Rsgi]]
[[Category: Rsgi]]
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[[Category: Structural genomic]]
 

Current revision

Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex

PDB ID 2dm6

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