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5vbc

From Proteopedia

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Current revision

Crystal structure of ATXR5 in complex with histone H3.1

Structural highlights

5vbc is a 4 chain structure with sequence from Arabidopsis thaliana and Ricinus communis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ATXR5_RICCO Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).

Publication Abstract from PubMed

In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.

Molecular basis for the methylation specificity of ATXR5 for histone H3.,Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF Nucleic Acids Res. 2017 Apr 5. doi: 10.1093/nar/gkx224. PMID:28383693^[1]

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

References

↑ Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF. Molecular basis for the methylation specificity of ATXR5 for histone H3. Nucleic Acids Res. 2017 Apr 5. doi: 10.1093/nar/gkx224. PMID:28383693 doi:http://dx.doi.org/10.1093/nar/gkx224

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Arabidopsis thaliana | Large Structures | Ricinus communis | Bergamin E | Couture J-F

@@ Line 3: / Line 3: @@
 <StructureSection load='5vbc' size='340' side='right'caption='[[5vbc]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5vbc]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VBC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VBC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5vbc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VBC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5va6|5va6]], [[5vab|5vab]], [[5vah|5vah]], [[5vac|5vac]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=5vbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbc OCA], [https://pdbe.org/5vbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vbc RCSB], [https://www.ebi.ac.uk/pdbsum/5vbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbc ProSAT]</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=5vbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbc OCA], [http://pdbe.org/5vbc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vbc RCSB], [http://www.ebi.ac.uk/pdbsum/5vbc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ATXR5_RICCO ATXR5_RICCO]] Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).
+[https://www.uniprot.org/uniprot/ATXR5_RICCO ATXR5_RICCO] Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Histone-lysine N-methyltransferase]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Bergamin, E]]
+[[Category: Ricinus communis]]
-[[Category: Couture, J F]]
+[[Category: Bergamin E]]
-[[Category: Methylation]]
+[[Category: Couture J-F]]
-[[Category: Nucleosome]]
-[[Category: Transferase-dna binding protein complex]]

5vbc

From Proteopedia

Current revision

Crystal structure of ATXR5 in complex with histone H3.1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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