5yko

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide

Structural highlights

5yko is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

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^[8]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jeong JH, Song HR, Ko JH, Jeong YM, Kwon YE, Seol JH, Amasino RM, Noh B, Noh YS. Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis. PLoS One. 2009 Nov 25;4(11):e8033. doi: 10.1371/journal.pone.0008033. PMID:19946624 doi:http://dx.doi.org/10.1371/journal.pone.0008033
↑ Lu F, Cui X, Zhang S, Liu C, Cao X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 2010 Mar;20(3):387-90. doi: 10.1038/cr.2010.27. Epub 2010 Feb 23. PMID:20177424 doi:http://dx.doi.org/10.1038/cr.2010.27
↑ Yang W, Jiang D, Jiang J, He Y. A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis. Plant J. 2010 May 1;62(4):663-73. doi: 10.1111/j.1365-313X.2010.04182.x. Epub, 2010 Feb 24. PMID:20202164 doi:http://dx.doi.org/10.1111/j.1365-313X.2010.04182.x
↑ Searle IR, Pontes O, Melnyk CW, Smith LM, Baulcombe DC. JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev. 2010 May 15;24(10):986-91. doi: 10.1101/gad.579910. PMID:20478993 doi:http://dx.doi.org/10.1101/gad.579910
↑ Deleris A, Greenberg MV, Ausin I, Law RW, Moissiard G, Schubert D, Jacobsen SE. Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep. 2010 Dec;11(12):950-5. doi: 10.1038/embor.2010.158. Epub 2010 Nov 5. PMID:21052090 doi:http://dx.doi.org/10.1038/embor.2010.158
↑ Ning YQ, Ma ZY, Huang HW, Mo H, Zhao TT, Li L, Cai T, Chen S, Ma L, He XJ. Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14. Nucleic Acids Res. 2015 Feb 18;43(3):1469-84. doi: 10.1093/nar/gku1382. Epub 2015, Jan 10. PMID:25578968 doi:http://dx.doi.org/10.1093/nar/gku1382
↑ Zhang S, Zhou B, Kang Y, Cui X, Liu A, Deleris A, Greenberg MV, Cui X, Qiu Q, Lu F, Wohlschlegel JA, Jacobsen SE, Cao X. C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. Cell Discov. 2015;1. doi: 10.1038/celldisc.2015.3. Epub 2015 Apr 28. PMID:26617990 doi:http://dx.doi.org/10.1038/celldisc.2015.3
↑ Yang Z, Qiu Q, Chen W, Jia B, Chen X, Hu H, He K, Deng X, Li S, Tao WA, Cao X, Du J. Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases. Plant Cell. 2017 Dec 12. pii: tpc.17.00666. doi: 10.1105/tpc.17.00666. PMID:29233856 doi:http://dx.doi.org/10.1105/tpc.17.00666

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5yko"

Categories: Arabidopsis thaliana | Large Structures | Du J | Yang Z

@@ Line 1: / Line 1: @@
 ==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=''>
+<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 [http://en.wikipedia.org/wiki/Arath Arath]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKO FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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='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='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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JMJ14, JMJ4, PKDM7B, At4g20400, F9F13.50 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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>
-<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=5yko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yko OCA], [http://pdbe.org/5yko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yko RCSB], [http://www.ebi.ac.uk/pdbsum/5yko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yko ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 ==
@@ Line 20: / Line 19: @@
 </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: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Du, J]]
+[[Category: Large Structures]]
-[[Category: Yang, Z]]
+[[Category: Du J]]
-[[Category: C5hc2 zinc finger]]
+[[Category: Yang Z]]
-[[Category: Gene regulation]]
-[[Category: H3k4me3 demethylase]]
-[[Category: Jmj14]]
-[[Category: Jumonji domain]]

5yko

From Proteopedia

Current revision

Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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