7feo: Difference between revisions

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<StructureSection load='7feo' size='340' side='right'caption='[[7feo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='7feo' size='340' side='right'caption='[[7feo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7feo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FEO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FEO FirstGlance]. <br>
<table><tr><td colspan='2'>[[7feo]] 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=7FEO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FEO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7feo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7feo OCA], [https://pdbe.org/7feo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7feo RCSB], [https://www.ebi.ac.uk/pdbsum/7feo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7feo 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=7feo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7feo OCA], [https://pdbe.org/7feo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7feo RCSB], [https://www.ebi.ac.uk/pdbsum/7feo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7feo ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/MBD5_ARATH MBD5_ARATH]] Transcriptional regulator that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. In addition, binds specifically methylated m(5)CpNpN but not m(5)CpNpG (N is A, T or C). Plays probably a role in gene silencing.<ref>PMID:12787239</ref> <ref>PMID:14605234</ref> <ref>PMID:15010609</ref> 
[[https://www.uniprot.org/uniprot/MBD5_ARATH MBD5_ARATH]] Transcriptional regulator that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. In addition, binds specifically methylated m(5)CpNpN but not m(5)CpNpG (N is A, T or C). Plays probably a role in gene silencing.<ref>PMID:12787239</ref> <ref>PMID:14605234</ref> <ref>PMID:15010609</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
13 MBD-containing genes (AtMBD1-13) have been identified in Arabidopsis thaliana so far, however, their DNA binding ability is still controversial. Here, we systematically measured the DNA binding affinities of these MBDs by ITC and EMSA binding assays, except for those of pseudogenes AtMBD3 and AtMBD13, and found that only AtMBD6 and AtMBD7 function as methylated DNA readers. We also found that the MBD of AtMBD5 exhibits very weak binding to methylated DNA compared to that of AtMBD6. To further investigate the structural basis of AtMBDs in binding to methylated DNA, we determined the complex structure of the AtMBD6 MBD with a 12mer mCG DNA and the apo structure of the AtMBD5 MBD. Structural analysis coupled with mutagenesis studies indicated that, in addition to the conserved arginine fingers contributing to the DNA binding specificity, the residues located in the loop1 and alpha1 are also essential for the methylated DNA binding of these MBDs in Arabidopsis thaliana, which explains why AtMBD5 MBD and the other AtMBDs display very weak or no binding to methylated DNA. Thus, our study here systematically demonstrates the DNA binding ability of the MBDs in Arabidopsis thaliana, which also provides a general guideline in understanding the DNA binding ability of the MBDs in other plants as a whole.
 
Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs.,Wu Z, Chen S, Zhou M, Jia L, Li Z, Zhang X, Min J, Liu K J Mol Biol. 2022 Jan 30;434(2):167404. doi: 10.1016/j.jmb.2021.167404. Epub 2021 , Dec 14. PMID:34919920<ref>PMID:34919920</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7feo" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Liu, K]]
[[Category: Liu K]]
[[Category: Min, J R]]
[[Category: Min JR]]
[[Category: Structural genomic]]
[[Category: Wu ZB]]
[[Category: Wu, Z B]]
[[Category: Zhou MQ]]
[[Category: Zhou, M Q]]
[[Category: Arabidopsis thaliana]]
[[Category: Dna binding protein]]
[[Category: Mbd domain]]
[[Category: Sgc]]
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