3q0b: Difference between revisions

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<StructureSection load='3q0b' size='340' side='right'caption='[[3q0b]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3q0b' size='340' side='right'caption='[[3q0b]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3q0b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q0B FirstGlance]. <br>
<table><tr><td colspan='2'>[[3q0b]] 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=3Q0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q0B FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 2.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q0c|3q0c]], [[3q0d|3q0d]], [[3q0f|3q0f]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At2g35160, SDG9, SET9, SUVH5, T4C15.17 ([https://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'>[https://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [https://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=3q0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q0b OCA], [https://pdbe.org/3q0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q0b RCSB], [https://www.ebi.ac.uk/pdbsum/3q0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q0b ProSAT]</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=3q0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q0b OCA], [https://pdbe.org/3q0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q0b RCSB], [https://www.ebi.ac.uk/pdbsum/3q0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q0b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SUVH5_ARATH SUVH5_ARATH]] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression.  
[https://www.uniprot.org/uniprot/SUVH5_ARATH SUVH5_ARATH] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cytosine DNA methylation is evolutionarily ancient, and in eukaryotes this epigenetic modification is associated with gene silencing. Proteins with SRA (SET- or RING-associated) methyl-binding domains are required for the establishment and/or maintenance of DNA methylation in both plants and mammals. The 5-methyl-cytosine (5mC)-binding specificity of several SRA domains have been characterized, and each one has a preference for DNA methylation in different sequence contexts. Here we demonstrate through mobility shift assays and calorimetric measurements that the SU(VAR)3-9 HOMOLOG 5 (SUVH5) SRA domain differs from other SRA domains in that it can bind methylated DNA in all contexts to similar extents. Crystal structures of the SUVH5 SRA domain bound to 5mC-containing DNA in either the fully or hemimethylated CG context or the methylated CHH context revealed a dual flip-out mechanism where both the 5mC and a base (5mC, C, or G, respectively) from the partner strand are simultaneously extruded from the DNA duplex and positioned within binding pockets of individual SRA domains. Our structure-based in vivo studies suggest that a functional SUVH5 SRA domain is required for both DNA methylation and accumulation of the H3K9 dimethyl modification in vivo, suggesting a role for the SRA domain in recruitment of SUVH5 to genomic loci.
 
A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo.,Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE Genes Dev. 2011 Jan 15;25(2):137-52. PMID:21245167<ref>PMID:21245167</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3q0b" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arath]]
[[Category: Arabidopsis thaliana]]
[[Category: Histone-lysine N-methyltransferase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Eerappa, R]]
[[Category: Eerappa R]]
[[Category: Patel, D J]]
[[Category: Patel DJ]]
[[Category: Simanshu, D K]]
[[Category: Simanshu DK]]
[[Category: 5mc binding protein]]
[[Category: Fully methylated cg]]
[[Category: Fully methylated cg duplex dna]]
[[Category: Sra]]
[[Category: Suvh5]]
[[Category: Transferase-dna complex]]

Revision as of 16:36, 1 March 2024

Crystal structure of SUVH5 SRA- fully methylated CG DNA complex in space group P42212Crystal structure of SUVH5 SRA- fully methylated CG DNA complex in space group P42212

Structural highlights

3q0b 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 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SUVH5_ARATH Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression.

See Also

3q0b, resolution 2.20Å

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