4iut: Difference between revisions

Line 1:

~~{{STRUCTURE_4iut| PDB=4iut | SCENE= }}~~

==crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide==

===crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide===

~~{{ABSTRACT_PUBMED_23636332}}~~

== Structural highlights ==

<table><tr><td colspan='2'>[[4iut]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IUT FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVM:CYMAL-4'>CVM</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=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g15215, F9L1.16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=4iut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iut OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4iut RCSB], [http://www.ebi.ac.uk/pdbsum/4iut PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.

~~==About this Structure==~~

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.,Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM, Strahl BD, Patel DJ, Jacobsen SE Nature. 2013 May 1. doi: 10.1038/nature12178. PMID:23636332<ref>PMID:23636332</ref>

~~[[4iut]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann.ac.il~~/~~oca-bin/ocashort?id=4IUT OCA].~~

==~~Reference~~==

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

~~<ref group="xtra">PMID:023636332</ref>~~<references ~~group="xtra"~~/><~~references~~/>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Arabidopsis thaliana]]

[[Category: Du, J.]]

[[Category: Du, J]]

[[Category: Patel, D J.]]

[[Category: Patel, D J]]

[[Category: Gene regulation]]

[[Category: H3k9me2]]

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@@ Line 1: / Line 1: @@
-{{STRUCTURE_4iut|  PDB=4iut  |  SCENE=  }}
+==crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide==
-===crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide===
+<StructureSection load='4iut' size='340' side='right' caption='[[4iut]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-{{ABSTRACT_PUBMED_23636332}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4iut]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IUT FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVM:CYMAL-4'>CVM</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=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4iup|4iup]], [[4iuq|4iuq]], [[4iur|4iur]], [[4iuv|4iuv]], [[4iuu|4iuu]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g15215, F9L1.16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=4iut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iut OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4iut RCSB], [http://www.ebi.ac.uk/pdbsum/4iut PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.
-==About this Structure==
+Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.,Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM, Strahl BD, Patel DJ, Jacobsen SE Nature. 2013 May 1. doi: 10.1038/nature12178. PMID:23636332<ref>PMID:23636332</ref>
-[[4iut]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUT OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:023636332</ref><references group="xtra"/><references/>
+</div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Du, J.]]
+[[Category: Du, J]]
-[[Category: Patel, D J.]]
+[[Category: Patel, D J]]
 [[Category: Gene regulation]]
 [[Category: H3k9me2]]