2vd7: Difference between revisions
New page: left|200px<br /><applet load="2vd7" size="350" color="white" frame="true" align="right" spinBox="true" caption="2vd7, resolution 2.25Å" /> '''CRYSTAL STRUCTURE OF... |
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== | ==Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid== | ||
<StructureSection load='2vd7' size='340' side='right'caption='[[2vd7]], [[Resolution|resolution]] 2.25Å' scene=''> | |||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25Å</td></tr> | |||
<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> | |||
<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> | |||
</table> | |||
== Function == | |||
[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> | |||
== 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/vd/2vd7_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/main_output.php?pdb_ID=2vd7 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2vd7" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Arrowsmith | [[Category: Arrowsmith CH]] | ||
[[Category: Edwards A]] | |||
[[Category: Edwards | [[Category: Kavanagh KL]] | ||
[[Category: Kavanagh | [[Category: McDonough MA]] | ||
[[Category: | [[Category: Ng SS]] | ||
[[Category: Ng | [[Category: Oppermann U]] | ||
[[Category: Oppermann | [[Category: Pilka ES]] | ||
[[Category: Pilka | [[Category: Savitsky P]] | ||
[[Category: Savitsky | [[Category: Schofield CJ]] | ||
[[Category: Schofield | [[Category: Sundstrom M]] | ||
[[Category: Sundstrom | [[Category: Weigelt J]] | ||
[[Category: Weigelt | [[Category: Von Delft F]] | ||
[[Category: | |||
