2ybp: Difference between revisions

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-[[Image:2ybp.png|left|200px]]
-<!--
+==JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)==
-The line below this paragraph, containing "STRUCTURE_2ybp", creates the "Structure Box" on the page.
+<StructureSection load='2ybp' size='340' side='right'caption='[[2ybp]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ybp]] is a 4 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=2YBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YBP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.02&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HG:(2R)-2-HYDROXYPENTANEDIOIC+ACID'>2HG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2ybp|  PDB=2ybp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ybp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ybp OCA], [https://pdbe.org/2ybp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ybp RCSB], [https://www.ebi.ac.uk/pdbsum/2ybp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ybp 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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mutations in isocitrate dehydrogenases (IDHs) have a gain-of-function effect leading to R(-)-2-hydroxyglutarate (R-2HG) accumulation. By using biochemical, structural and cellular assays, we show that either or both R- and S-2HG inhibit 2-oxoglutarate (2OG)-dependent oxygenases with varying potencies. Half-maximal inhibitory concentration (IC(50)) values for the R-form of 2HG varied from approximately 25 muM for the histone N(varepsilon)-lysine demethylase JMJD2A to more than 5 mM for the hypoxia-inducible factor (HIF) prolyl hydroxylase. The results indicate that candidate oncogenic pathways in IDH-associated malignancy should include those that are regulated by other 2OG oxygenases than HIF hydroxylases, in particular those involving the regulation of histone methylation.
-===JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36ME3 PEPTIDE (30-41)===
+The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.,Chowdhury R, Yeoh KK, Tian YM, Hillringhaus L, Bagg EA, Rose NR, Leung IK, Li XS, Woon EC, Yang M, McDonough MA, King ON, Clifton IJ, Klose RJ, Claridge TD, Ratcliffe PJ, Schofield CJ, Kawamura A EMBO Rep. 2011 May 1;12(5):463-9. Epub 2011 Apr 1. PMID:21460794<ref>PMID:21460794</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ybp" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21460794}}, adds the Publication Abstract to the page
+*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21460794 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21460794}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[2ybp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YBP OCA].
-==Reference==
-<ref group="xtra">PMID:021460794</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Chowdhury, R.]]
+[[Category: Large Structures]]
-[[Category: Mcdonough, M A.]]
+[[Category: Chowdhury R]]
-[[Category: Schofield, C J.]]
+[[Category: McDonough MA]]
+[[Category: Schofield CJ]]