2vd7

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{{STRUCTURE_2vd7| PDB=2vd7 | SCENE= }}
 
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===Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid===
 
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{{ABSTRACT_PUBMED_18942826}}
 
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==About this Structure==
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==Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid==
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[[2vd7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VD7 OCA].
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<StructureSection load='2vd7' size='340' side='right'caption='[[2vd7]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2vd7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VD7 FirstGlance]. <br>
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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]] 2.25&#8491;</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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PD2:PYRIDINE-2,4-DICARBOXYLIC+ACID'>PD2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2vd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vd7 OCA], [https://pdbe.org/2vd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vd7 RCSB], [https://www.ebi.ac.uk/pdbsum/2vd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vd7 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>
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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/vd/2vd7_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=2vd7 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 dynamic methylation of histone lysyl residues plays an important role in biology by regulating transcription, maintaining genomic integrity, and by contributing to epigenetic effects. Here we describe a variety of inhibitor scaffolds that inhibit the human 2-oxoglutarate-dependent JMJD2 subfamily of histone demethylases. Combined with structural data, these chemical starting points will be useful to generate small-molecule probes to analyze the physiological roles of these enzymes in epigenetic signaling.
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==Reference==
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Inhibitor scaffolds for 2-oxoglutarate-dependent histone lysine demethylases.,Rose NR, Ng SS, Mecinovic J, Lienard BM, Bello SH, Sun Z, McDonough MA, Oppermann U, Schofield CJ J Med Chem. 2008 Nov 27;51(22):7053-6. doi: 10.1021/jm800936s. PMID:18942826<ref>PMID:18942826</ref>
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<ref group="xtra">PMID:018942826</ref><references group="xtra"/><references/>
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[[Category: Human]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Arrowsmith, C H.]]
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</div>
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[[Category: Delft, F von]]
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<div class="pdbe-citations 2vd7" style="background-color:#fffaf0;"></div>
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[[Category: Edwards, A.]]
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[[Category: Kavanagh, K L.]]
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==See Also==
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[[Category: McDonough, M A.]]
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*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
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[[Category: Ng, S S.]]
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== References ==
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[[Category: Oppermann, U.]]
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<references/>
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[[Category: Pilka, E S.]]
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__TOC__
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[[Category: Savitsky, P.]]
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</StructureSection>
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[[Category: Schofield, C J.]]
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[[Category: Homo sapiens]]
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[[Category: Sundstrom, M.]]
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[[Category: Large Structures]]
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[[Category: Weigelt, J.]]
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[[Category: Arrowsmith CH]]
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[[Category: Chromatin regulator]]
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[[Category: Edwards A]]
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[[Category: Dioxygenase]]
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[[Category: Kavanagh KL]]
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[[Category: Histone demethylation inhibitor jmjc domain]]
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[[Category: McDonough MA]]
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[[Category: Host-virus interaction]]
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[[Category: Ng SS]]
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[[Category: Iron]]
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[[Category: Oppermann U]]
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[[Category: Metal-binding]]
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[[Category: Pilka ES]]
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[[Category: Nucleus]]
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[[Category: Savitsky P]]
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[[Category: Oxidoreductase]]
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[[Category: Schofield CJ]]
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[[Category: Phosphorylation]]
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[[Category: Sundstrom M]]
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[[Category: Transcription]]
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[[Category: Weigelt J]]
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[[Category: Transcription regulation]]
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[[Category: Von Delft F]]
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[[Category: Zinc-finger]]
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Current revision

Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid

PDB ID 2vd7

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