5yvx

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide

Structural highlights

5yvx 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 1.591Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ASHH2_ARATH Histone methyltransferase involved in di and tri-methylation of 'Lys-36' of histone H3 (H3K36me2 and H3K36me3). Binds to H3 already mono- or di-methylated on 'Lys-4'(H3K4me1 or H3K4me2), but not to H3K4me3. H3K4me and H3K36me represent specific tags for epigenetic transcriptional activation. Regulates positively FLC transcription to prevent early flowering transition. Required for flowering transition in response to vernalization and for the maintenance of FLC expression in late embryos, but dispensable for the initial reactivation in early embryos during reprogramming. Seems also to modulate several traits including floral organ size, root size and dormancy. Promotes apical dominance (PubMed:16299497, PubMed:10518493, PubMed:16258034, PubMed:18070919, PubMed:19915673, PubMed:20711170). Directly involved in the tri-methylation of 'Lys-36' of histone H3 (H3K36me3) at LAZ5 chromatin to maintain a transcriptionally active state of LAZ5, a TIR-NB-LRR protein involved in innate immunity (PubMed:20949080).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

Chromatin consists of DNA and histones, and specific histone modifications that determine chromatin structure and activity are regulated by three types of proteins, called writer, reader and eraser. Histone reader proteins from vertebrates, vertebrate-infecting parasites, and higher plants possess a CW domain, which has been reported to read histone H3 lysine 4 (H3K4). The CW domain of Arabidopsis SDG8 (also called ASHH2), a histone H3 lysine 36 methyltransferase, preferentially binds monomethylated H3K4 (H3K4me1), unlike the mammalian CW domain protein which binds trimethylated H3K4 (H3K4me3). However, the molecular basis of the selective binding by the SDG8 CW domain (SDG8-CW) remains unclear. Here, we solved the 1.6 A resolution structure of SDG8-CW in complex with H3K4me1, which revealed that residues in the C-terminal alpha helix of SDG8-CW determine binding specificity for low methylation levels at H3K4. Moreover, substitutions of key residues, specifically Ile915 and Asn916, converted SDG8-CW binding preference from H3K4me1 to H3K4me3. Sequence alignments and mutagenesis studies revealed that the CW domain of SDG725, the homolog of SDG8 in rice, shares the same binding preference with SDG8-CW, indicating that preference for low-methylated H3K4 by the CW domain of ASHH2 homologs is conserved among higher-order plants. Our findings provide first structural insights into the molecular basis for specific recognition of monomethylated H3K4 by the H3K4me1 reader protein SDG8 from Arabidopsis.

Uncovering the mechanistic basis for specific recognition of monomethylated H3K4 by the CW domain of Arabidopsis histone methyltransferase SDG8.,Liu Y, Huang Y J Biol Chem. 2018 Mar 1. pii: RA117.001390. doi: 10.1074/jbc.RA117.001390. PMID:29496997^[8]

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

References

↑ Soppe WJ, Bentsink L, Koornneef M. The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana. Development. 1999 Nov;126(21):4763-70. PMID:10518493
↑ Kim SY, He Y, Jacob Y, Noh YS, Michaels S, Amasino R. Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell. 2005 Dec;17(12):3301-10. Epub 2005 Oct 28. PMID:16258034 doi:http://dx.doi.org/10.1105/tpc.105.034645
↑ Zhao Z, Yu Y, Meyer D, Wu C, Shen WH. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nat Cell Biol. 2005 Dec;7(12):1256-60. Epub 2005 Nov 20. PMID:16299497 doi:http://dx.doi.org/10.1038/ncb1329
↑ Xu L, Zhao Z, Dong A, Soubigou-Taconnat L, Renou JP, Steinmetz A, Shen WH. Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana. Mol Cell Biol. 2008 Feb;28(4):1348-60. Epub 2007 Dec 10. PMID:18070919 doi:http://dx.doi.org/10.1128/MCB.01607-07
↑ Grini PE, Thorstensen T, Alm V, Vizcay-Barrena G, Windju SS, Jorstad TS, Wilson ZA, Aalen RB. The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis. PLoS One. 2009 Nov 12;4(11):e7817. doi: 10.1371/journal.pone.0007817. PMID:19915673 doi:http://dx.doi.org/10.1371/journal.pone.0007817
↑ Ko JH, Mitina I, Tamada Y, Hyun Y, Choi Y, Amasino RM, Noh B, Noh YS. Growth habit determination by the balance of histone methylation activities in Arabidopsis. EMBO J. 2010 Sep 15;29(18):3208-15. doi: 10.1038/emboj.2010.198. Epub 2010 Aug, 13. PMID:20711170 doi:http://dx.doi.org/10.1038/emboj.2010.198
↑ Palma K, Thorgrimsen S, Malinovsky FG, Fiil BK, Nielsen HB, Brodersen P, Hofius D, Petersen M, Mundy J. Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog. 2010 Oct 7;6(10):e1001137. doi: 10.1371/journal.ppat.1001137. PMID:20949080 doi:http://dx.doi.org/10.1371/journal.ppat.1001137
↑ Liu Y, Huang Y. Uncovering the mechanistic basis for specific recognition of monomethylated H3K4 by the CW domain of Arabidopsis histone methyltransferase SDG8. J Biol Chem. 2018 Mar 1. pii: RA117.001390. doi: 10.1074/jbc.RA117.001390. PMID:29496997 doi:http://dx.doi.org/10.1074/jbc.RA117.001390

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/5yvx"

Categories: Arabidopsis thaliana | Large Structures | Huang Y | Liu Y

@@ Line 1: / Line 1: @@
 ==Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide==
-<StructureSection load='5yvx' size='340' side='right' caption='[[5yvx]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
+<StructureSection load='5yvx' size='340' side='right'caption='[[5yvx]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yvx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yvx]] 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=5YVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YVX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.591&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=5yvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvx OCA], [https://pdbe.org/5yvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yvx RCSB], [https://www.ebi.ac.uk/pdbsum/5yvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvx 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=5yvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvx OCA], [http://pdbe.org/5yvx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvx RCSB], [http://www.ebi.ac.uk/pdbsum/5yvx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ASHH2_ARATH ASHH2_ARATH]] Histone methyltransferase involved in di and tri-methylation of 'Lys-36' of histone H3 (H3K36me2 and H3K36me3). Binds to H3 already mono- or di-methylated on 'Lys-4'(H3K4me1 or H3K4me2), but not to H3K4me3. H3K4me and H3K36me represent specific tags for epigenetic transcriptional activation. Regulates positively FLC transcription to prevent early flowering transition. Required for flowering transition in response to vernalization and for the maintenance of FLC expression in late embryos, but dispensable for the initial reactivation in early embryos during reprogramming. Seems also to modulate several traits including floral organ size, root size and dormancy. Promotes apical dominance (PubMed:16299497, PubMed:10518493, PubMed:16258034, PubMed:18070919, PubMed:19915673, PubMed:20711170). Directly involved in the tri-methylation of 'Lys-36' of histone H3 (H3K36me3) at LAZ5 chromatin to maintain a transcriptionally active state of LAZ5, a TIR-NB-LRR protein involved in innate immunity (PubMed:20949080).<ref>PMID:10518493</ref> <ref>PMID:16258034</ref> <ref>PMID:16299497</ref> <ref>PMID:18070919</ref> <ref>PMID:19915673</ref> <ref>PMID:20711170</ref> <ref>PMID:20949080</ref>
+[https://www.uniprot.org/uniprot/ASHH2_ARATH ASHH2_ARATH] Histone methyltransferase involved in di and tri-methylation of 'Lys-36' of histone H3 (H3K36me2 and H3K36me3). Binds to H3 already mono- or di-methylated on 'Lys-4'(H3K4me1 or H3K4me2), but not to H3K4me3. H3K4me and H3K36me represent specific tags for epigenetic transcriptional activation. Regulates positively FLC transcription to prevent early flowering transition. Required for flowering transition in response to vernalization and for the maintenance of FLC expression in late embryos, but dispensable for the initial reactivation in early embryos during reprogramming. Seems also to modulate several traits including floral organ size, root size and dormancy. Promotes apical dominance (PubMed:16299497, PubMed:10518493, PubMed:16258034, PubMed:18070919, PubMed:19915673, PubMed:20711170). Directly involved in the tri-methylation of 'Lys-36' of histone H3 (H3K36me3) at LAZ5 chromatin to maintain a transcriptionally active state of LAZ5, a TIR-NB-LRR protein involved in innate immunity (PubMed:20949080).<ref>PMID:10518493</ref> <ref>PMID:16258034</ref> <ref>PMID:16299497</ref> <ref>PMID:18070919</ref> <ref>PMID:19915673</ref> <ref>PMID:20711170</ref> <ref>PMID:20949080</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 5yvx" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Histone-lysine N-methyltransferase]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Huang, Y]]
+[[Category: Large Structures]]
-[[Category: Liu, Y]]
+[[Category: Huang Y]]
-[[Category: Cw domain]]
+[[Category: Liu Y]]
-[[Category: H3k4me1]]
-[[Category: Sdg8]]
-[[Category: Transferase]]

5yvx

From Proteopedia

Current revision

Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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