2q8e: Difference between revisions

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-{{Seed}}
-[[Image:2q8e.png|left|200px]]
-<!--
+==Specificity and Mechanism of JMJD2A, a Trimethyllysine-Specific Histone Demethylase==
-The line below this paragraph, containing "STRUCTURE_2q8e", creates the "Structure Box" on the page.
+<StructureSection load='2q8e' size='340' side='right'caption='[[2q8e]], [[Resolution|resolution]] 2.05&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'>[[2q8e]] 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=2Q8E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q8E 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]] 2.05&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</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>
-{{STRUCTURE_2q8e|  PDB=2q8e  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q8e OCA], [https://pdbe.org/2q8e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q8e RCSB], [https://www.ebi.ac.uk/pdbsum/2q8e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q8e 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/q8/2q8e_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=2q8e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+JMJD2A is a JmjC histone demethylase (HDM) that catalyzes the demethylation of di- and trimethylated Lys9 and Lys36 in histone H3 (H3K9me2/3 and H3K36me2/3). Here we present the crystal structures of the JMJD2A catalytic domain in complex with H3K9me3, H3K36me2 and H3K36me3 peptides. The structures reveal that histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated epsilon-ammonium cation is coordinated within a methylammonium-binding pocket through carbon-oxygen (CH...O) hydrogen bonds that position one of the zeta-methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation. Mutations of the residues comprising this pocket abrogate demethylation by JMJD2A, with the exception of an S288A substitution, which augments activity, particularly toward H3K9me2. We propose that this residue modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs.
-===Specificity and Mechanism of JMJD2A, a Trimethyllysine-Specific Histone Demethylase===
+Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase.,Couture JF, Collazo E, Ortiz-Tello PA, Brunzelle JS, Trievel RC Nat Struct Mol Biol. 2007 Aug;14(8):689-95. Epub 2007 Jun 24. PMID:17589523<ref>PMID:17589523</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2q8e" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17589523}}, 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 17589523 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17589523}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Q8E is a [[Single protein]] structure of 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=2Q8E OCA].
-==Reference==
-Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase., Couture JF, Collazo E, Ortiz-Tello PA, Brunzelle JS, Trievel RC, Nat Struct Mol Biol. 2007 Aug;14(8):689-95. Epub 2007 Jun 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17589523 17589523]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Brunzelle, J S.]]
+[[Category: Brunzelle JS]]
-[[Category: Collazo, E.]]
+[[Category: Collazo E]]
-[[Category: Couture, J-F.]]
+[[Category: Couture J-F]]
-[[Category: Ortiz-Tello, P.]]
+[[Category: Ortiz-Tello P]]
-[[Category: Trievel, R C.]]
+[[Category: Trievel RC]]
-[[Category: Histone demethylase]]
-[[Category: Hydroxylase]]
-[[Category: N-oxalylglycine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 06:07:33 2008''