4iup: Difference between revisions

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-{{STRUCTURE_4iup|  PDB=4iup  |  SCENE=  }}
-===crystal structure of Se-substituted arabidopsis thaliana SHH1 SAWADEE domain L200M/L218M mutant===
-{{ABSTRACT_PUBMED_23636332}}
-==About this Structure==
+==crystal structure of Se-substituted arabidopsis thaliana SHH1 SAWADEE domain L200M/L218M mutant==
-[[4iup]] is a 2 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=4IUP OCA].
+<StructureSection load='4iup' size='340' side='right'caption='[[4iup]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4iup]] 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=4IUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IUP FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CVM:CYMAL-4'>CVM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4iup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iup OCA], [https://pdbe.org/4iup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iup RCSB], [https://www.ebi.ac.uk/pdbsum/4iup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iup ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SHH1_ARATH SHH1_ARATH] Involved in RNA-directed DNA methylation (RdDM). Required for the silencing of some endogenous RdDM targets and accumulation of 24-nt siRNAs, but not for the production of Pol V-dependent transcripts. Functions in transcriptional silencing through both DNA methylation-dependent and -independent pathways. Required for both maintenance and de-novo DNA methylation. Plays a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM.<ref>PMID:21811420</ref> <ref>PMID:22064704</ref> <ref>PMID:23636332</ref> <ref>PMID:23637343</ref>
+<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.
-==Reference==
+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>
-<ref group="xtra">PMID:023636332</ref><references group="xtra"/><references/>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4iup" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Du, J.]]
+[[Category: Large Structures]]
-[[Category: Patel, D J.]]
+[[Category: Du J]]
-[[Category: Dna binding protein]]
+[[Category: Patel DJ]]
-[[Category: Gene regulation]]
-[[Category: Histone]]
-[[Category: Mediate interaction]]
-[[Category: Tandem tudor]]
-[[Category: Zinc finger]]