6h8p: Difference between revisions
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The | ==JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)== | ||
<StructureSection load='6h8p' size='340' side='right' caption='[[6h8p]], [[Resolution|resolution]] 1.98Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6h8p]] is a 4 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=6H8P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H8P FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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 id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6h8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h8p OCA], [http://pdbe.org/6h8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h8p RCSB], [http://www.ebi.ac.uk/pdbsum/6h8p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h8p ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://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> [[http://www.uniprot.org/uniprot/H14_HUMAN H14_HUMAN]] Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity). | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
N-Methylation of lysyl residues is widely observed on histone proteins. Using isolated enzymes, we report mechanistic and structural studies on histone lysine demethylase (KDM)-catalysed demethylation of N(epsilon) -methylated lysine 26 on histone 1 isotype 4 (H1.4). The results reveal that methylated H1.4K26 is a substrate for all members of the KDM4 subfamily and that KDM4A-catalysed demethylation of H1.4K26me3 peptide is similarly efficient to that of H3K9me3. Crystallographic studies of an H1.4K26me3:KDM4A complex reveal a conserved binding geometry to that of H3K9me3. In light of the high activity of the KDM4s on this mark, our results suggest JmjC KDM-catalysed demethylation of H1.4K26 may be as prevalent as demethylation on the H3 tail and warrants further investigation in cells. This article is protected by copyright. All rights reserved. | |||
Mechanistic and Structural Studies of KDM-Catalysed Demethylation of Histone 1 Isotype 4 at Lysine 26.,Walport LJ, Hopkinson RJ, Chowdhury R, Zhang Y, Bonnici J, Schiller R, Kawamura A, Schofield CJ FEBS Lett. 2018 Aug 29. doi: 10.1002/1873-3468.13231. PMID:30156264<ref>PMID:30156264</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6h8p" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Human]] | |||
[[Category: Chowdhury, R]] | [[Category: Chowdhury, R]] | ||
[[Category: Schofield, C | [[Category: Schofield, C J]] | ||
[[Category: Walport, L | [[Category: Walport, L J]] | ||
[[Category: 2-oxoglutarate]] | |||
[[Category: Chromatin regulator]] | |||
[[Category: Demethylase]] | |||
[[Category: Dioxygenase]] | |||
[[Category: Double-stranded beta helix]] | |||
[[Category: Dsbh]] | |||
[[Category: Epigenetic and transcription regulation]] | |||
[[Category: Facial triad]] | |||
[[Category: Histone]] | |||
[[Category: Hydroxylation]] | |||
[[Category: Iron]] | |||
[[Category: Jmjc domain]] | |||
[[Category: Jmjd2a]] | |||
[[Category: Kdm4a]] | |||
[[Category: Metal binding protein]] | |||
[[Category: Non-heme]] | |||
[[Category: Oxidoreductase]] | |||
[[Category: Oxygenase]] | |||
Latest revision as of 07:56, 12 September 2018
JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
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