1khc: Difference between revisions

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-[[Image:1khc.jpg|left|200px]]<br /><applet load="1khc" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1khc, resolution 1.8&Aring;" />
-'''Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b'''<br />
-==Overview==
+==Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b==
-The PWWP domain is a weakly conserved sequence motif found in &gt; 60 eukaryotic proteins, including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain other chromatin-association domains. A 135-residue PWWP domain from mouse Dnmt3b (amino acids 223--357) has been structurally characterized at 1.8 A resolution. The N-terminal half of this domain resembles a barrel-like five-stranded structure, whereas the C-terminal half contains a five-helix bundle. The two halves are packed against each other to form a single structural module that exhibits a prominent positive electrostatic potential. The PWWP domain alone binds DNA in vitro, probably through its basic surface. We also show that recombinant Dnmt3b2 protein (a splice variant of Dnmt3b) and two N-terminal deletion mutants (Delta218 and Delta369) have approximately equal methyl transfer activity on unmethylated and hemimethylated CpG-containing oligonucleotides. The Delta218 protein, which includes the PWWP domain, binds DNA more strongly than Delta369, which lacks the PWWP domain.
+<StructureSection load='1khc' size='340' side='right'caption='[[1khc]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1khc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KHC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=1khc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1khc OCA], [https://pdbe.org/1khc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1khc RCSB], [https://www.ebi.ac.uk/pdbsum/1khc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1khc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DNM3B_MOUSE DNM3B_MOUSE] Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing. In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Function as transcriptional corepressor by associating with ZHX1 (By similarity).<ref>PMID:10555141</ref> <ref>PMID:11919202</ref> <ref>PMID:16567415</ref> <ref>PMID:18056424</ref> <ref>PMID:18567530</ref> <ref>PMID:11836534</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/1khc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1khc ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-KHC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=UNX:'>UNX</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHC OCA].
+*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
+== References ==
-==Reference==
+<references/>
-The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds., Qiu C, Sawada K, Zhang X, Cheng X, Nat Struct Biol. 2002 Mar;9(3):217-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11836534 11836534]
+__TOC__
-[[Category: DNA (cytosine-5-)-methyltransferase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Cheng X]]
-[[Category: Cheng, X.]]
+[[Category: Qiu C]]
-[[Category: Qiu, C.]]
+[[Category: Sawada K]]
-[[Category: Sawada, K.]]
+[[Category: Zhang X]]
-[[Category: Zhang, X.]]
-[[Category: UNX]]
-[[Category: five beta-sheets barrel followed by five-helix bundle]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:34:09 2008''