5zwi

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==Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group==
==Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group==
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<StructureSection load='5zwi' size='340' side='right' caption='[[5zwi]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='5zwi' size='340' side='right'caption='[[5zwi]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5zwi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZWI FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5zwi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZWI FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KX:(2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one'>9KX</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<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=5zwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwi OCA], [http://pdbe.org/5zwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zwi RCSB], [http://www.ebi.ac.uk/pdbsum/5zwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwi ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9KX:(2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one'>9KX</scene></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=5zwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwi OCA], [https://pdbe.org/5zwi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zwi RCSB], [https://www.ebi.ac.uk/pdbsum/5zwi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwi ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>
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[https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We designed and synthesized vitamin D analogues with an electrophile as covalent modifiers for the vitamin D receptor (VDR). Novel vitamin D analogues 1-4 have an electrophilic enone group at the side chain for conjugate addition to His301 or His393 in the VDR. All compounds showed specific VDR-binding potency and agonistic activity. Covalent bond formations of 1-4 with the ligand-binding domain (LBD) of VDR were evaluated by electrospray ionization mass spectrometry. All compounds were shown to covalently bind to the VDR-LBD, and the abundance of VDR-LBD corresponding conjugate adducts of 1-4 increased with incubation time. Enone compounds 1 and 2 showed higher reactivity than the ene-ynone 3 and dienone 4 compounds. Furthermore, we successfully obtained cocrystals of VDR-LBD with analogues 1-4. X-ray crystallographic analysis showed a covalent bond with His301 in VDR-LBD. We successfully synthesized vitamin D analogues that form a covalent bond with VDR-LBD.
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Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands.,Yoshizawa M, Itoh T, Hori T, Kato A, Anami Y, Yoshimoto N, Yamamoto K J Med Chem. 2018 Jul 11. doi: 10.1021/acs.jmedchem.8b00774. PMID:29936834<ref>PMID:29936834</ref>
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==See Also==
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*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
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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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<div class="pdbe-citations 5zwi" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Anami, Y]]
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[[Category: Homo sapiens]]
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[[Category: Itoh, T]]
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[[Category: Large Structures]]
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[[Category: Kato, A]]
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[[Category: Rattus norvegicus]]
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[[Category: Yamamoto, K]]
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[[Category: Anami Y]]
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[[Category: Yoshimoto, N]]
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[[Category: Itoh T]]
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[[Category: Yoshizawa, M]]
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[[Category: Kato A]]
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[[Category: Hormone]]
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[[Category: Yamamoto K]]
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[[Category: Hormone covalent modifier transcription factor vitamind3 enone michael addition electrophile]]
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[[Category: Yoshimoto N]]
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[[Category: Yoshizawa M]]

Current revision

Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group

PDB ID 5zwi

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