View source for 5yko


==Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide==
<StructureSection load='5yko' size='340' side='right'caption='[[5yko]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5yko]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YKO 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]] 2.9&#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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5yko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yko OCA], [https://pdbe.org/5yko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yko RCSB], [https://www.ebi.ac.uk/pdbsum/5yko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yko ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/JMJ14_ARATH JMJ14_ARATH] Transcriptional repressor (PubMed:25578968). Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a higher activity for H3K4me3 and H3K4me2 than H3K4me1. No activity on H3K9me3/2, H3K36me3/2 and H3K27me3/2. Represses FT and TSF expression to inhibit the floral transition. Binds around the transcription start site of the FT locus. Involved in the DRM2-mediated maintenance of DNA methylation, but not required for the de novo DNA methylation. Required for demethylating histone H3K4me3 at the target of RNA silencing. Together with NAC051/NAC052 and NAC050, regulates gene expression and flowering time, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968).<ref>PMID:19946624</ref> <ref>PMID:20177424</ref> <ref>PMID:20202164</ref> <ref>PMID:20478993</ref> <ref>PMID:21052090</ref> <ref>PMID:25578968</ref> <ref>PMID:26617990</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In chromatin, histone methylation affects the epigenetic regulation of multiple processes in animals and plants and is modulated by the activities of histone methyltransferases and histone demethylases. The jumonji domain-containing histone demethylases have diverse functions and can be classified into several subfamilies. In humans, the jumonji domain-containing Lysine (K)-Specific Demethylase 5/Jumonji and ARID Domain Protein (KDM5/JARID) subfamily demethylases are specific for histone 3 lysine 4 trimethylation (H3K4me3) and are important drug targets for cancer treatment. In Arabidopsis thaliana, the KDM5/JARID subfamily H3K4me3 demethylase JUMONJI 14 (JMJ14) plays important roles in flowering, gene silencing, and DNA methylation. Here, we report the crystal structures of the JMJ14 catalytic domain in both substrate-free and bound forms. The structures reveal that the jumonji and C5HC2 domains contribute to the specific recognition of the H3R2 and H3Q5 to facilitate H3K4me3 substrate specificity. The critical acidic residues are conserved in plants and animals with the corresponding mutations impairing the enzyme activity of both JMJ14 and human KDM5B, indicating a common substrate recognition mechanism for KDM5 subfamily demethylases shared by plants and animals and further informing efforts to design targeted inhibitors of human KDM5.

Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases.,Yang Z, Qiu Q, Chen W, Jia B, Chen X, Hu H, He K, Deng X, Li S, Tao WA, Cao X, Du J Plant Cell. 2017 Dec 12. pii: tpc.17.00666. doi: 10.1105/tpc.17.00666. PMID:29233856<ref>PMID:29233856</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5yko" style="background-color:#fffaf0;"></div>

==See Also==
*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Du J]]
[[Category: Yang Z]]