6qxz

From Proteopedia

(Difference between revisions)

Current revision

Solution structure of the ASHH2 CW domain with the N-terminal histone H3 tail mimicking peptide monomethylated on lysine 4

Structural highlights

6qxz is a 2 chain structure with sequence from Arabidopsis thaliana and Homo sapiens. This structure supersedes the now removed PDB entry 6hbo. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
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 post-translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N-terminal tail lysine residues constitutes one of many such modifications, executed by families of histone lysine methyltransferase (HKMTase). One such protein is ASHH2 from the flowering plant Arabidopsis thaliana, equipped with the interaction domain, CW, and the HKMTase domain, SET. The CW domain of ASHH2 is a selective binder of monomethylation at lysine 4 on histone H3 (H3K4me1) and likely helps the enzyme dock correctly onto chromatin sites. The study of CW and related interaction domains has so far been emphasizing lock-key models, missing important aspects of histone-tail CW interactions. We here present an analysis of the ASHH2 CW-H3K4me1 complex using NMR and molecular dynamics, as well as mutation and affinity studies of flexible coils. beta-augmentation and rearrangement of coils coincide with changes in the flexibility of the complex, in particular the eta1, eta3 and C-terminal coils, but also in the beta1 and beta2 strands and the C-terminal part of the ligand. Furthermore, we show that mutating residues with outlier dynamic behaviour affect the complex binding affinity despite these not being in direct contact with the ligand. Overall, the binding process is consistent with conformational selection. We propose that this binding mechanism presents an advantage when searching for the correct post-translational modification state among the highly modified and flexible histone tails, and also that the binding shifts the catalytic SET domain towards the nucleosome. DATABASES: Structural data are available in the PDB database under the accession code 6QXZ. Resonance assignments for CW42 in its apo- and holo-forms are available in the BMRB database under the accession code 27251.

The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection.,Dobrovolska O, Brilkov M, Madeleine N, Odegard-Fougner O, Stromland O, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau O FEBS J. 2020 Oct;287(20):4458-4480. doi: 10.1111/febs.15256. Epub 2020 Mar 24. PMID:32083791^[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
↑ Dobrovolska O, Brilkov M, Madeleine N, Odegard-Fougner O, Stromland O, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau O. The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. FEBS J. 2020 Oct;287(20):4458-4480. doi: 10.1111/febs.15256. Epub 2020 Mar 24. PMID:32083791 doi:http://dx.doi.org/10.1111/febs.15256

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/6qxz"

@@ Line 1: / Line 1: @@
 ==Solution structure of the ASHH2 CW domain with the N-terminal histone H3 tail mimicking peptide monomethylated on lysine 4==
-<StructureSection load='6qxz' size='340' side='right'caption='[[6qxz]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='6qxz' size='340' side='right'caption='[[6qxz]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6qxz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6hbo 6hbo]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QXZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6QXZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6qxz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6hbo 6hbo]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QXZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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='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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6qxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qxz OCA], [https://pdbe.org/6qxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qxz RCSB], [https://www.ebi.ac.uk/pdbsum/6qxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qxz ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ASHH2, EFS, LAZ2, SDG8, SET8, At1g77300, T14N5.15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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'>[http://proteopedia.org/fgij/fg.htm?mol=6qxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qxz OCA], [http://pdbe.org/6qxz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qxz RCSB], [http://www.ebi.ac.uk/pdbsum/6qxz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qxz 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 29: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Histone-lysine N-methyltransferase]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Dobrovolska, O]]
+[[Category: Bril'kov M]]
-[[Category: Halskau, O]]
+[[Category: Dobrovolska O]]
-[[Category: Madeleine, N]]
+[[Category: Halskau O]]
-[[Category: Teigen, K]]
+[[Category: Madeleine N]]
-[[Category: Kov, M Bril]]
+[[Category: Teigen K]]
-[[Category: Plant protein]]
-[[Category: Transferase]]

6qxz

From Proteopedia

Current revision

Solution structure of the ASHH2 CW domain with the N-terminal histone H3 tail mimicking peptide monomethylated on lysine 4

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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