2ox0: Difference between revisions

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 ==Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9==
-<StructureSection load='2ox0' size='340' side='right' caption='[[2ox0]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='2ox0' size='340' side='right'caption='[[2ox0]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ox0]] 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=2OX0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OX0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ox0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OX0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OX0 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2oq6|2oq6]], [[2oq7|2oq7]], [[2os2|2os2]], [[2ot7|2ot7]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2oq6|2oq6]], [[2oq7|2oq7]], [[2os2|2os2]], [[2ot7|2ot7]]</div></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JMJD2A, JHDM3A, JMJD2, KIAA0677 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JMJD2A, JHDM3A, JMJD2, KIAA0677 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ox0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ox0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ox0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ox0 PDBsum]</span></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=2ox0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ox0 OCA], [https://pdbe.org/2ox0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ox0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ox0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ox0 ProSAT]</span></td></tr>
-<table>
+</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/ox/2ox0_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ox/2ox0_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2ox0 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 30: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2ox0" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Jumonji domain-containing protein 2A|Jumonji domain-containing protein 2A]]
+*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
+[[Category: Human]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Large Structures]]
-[[Category: Delft, F von.]]
+[[Category: Arrowsmith, C H]]
-[[Category: Edwards, A.]]
+[[Category: Delft, F von]]
-[[Category: Kavanagh, K L.]]
+[[Category: Edwards, A]]
-[[Category: McDonough, M A.]]
+[[Category: Kavanagh, K L]]
-[[Category: Ng, S S.]]
+[[Category: McDonough, M A]]
-[[Category: Oppermann, U.]]
+[[Category: Ng, S S]]
-[[Category: Pilka, E S.]]
+[[Category: Oppermann, U]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Pilka, E S]]
-[[Category: Savitsky, P.]]
+[[Category: Structural genomic]]
-[[Category: Schofield, C J.]]
+[[Category: Savitsky, P]]
-[[Category: Sundstrom, M.]]
+[[Category: Schofield, C J]]
-[[Category: Weigelt, J.]]
+[[Category: Sundstrom, M]]
+[[Category: Weigelt, J]]
 [[Category: Demethylase]]
 [[Category: Double-stranded beta helix]]
@@ Line 53: / Line 58: @@
 [[Category: Oxygenase]]
 [[Category: Sgc]]
-[[Category: Structural genomic]]
-[[Category: Structural genomics consortium]]