1khc: Difference between revisions

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[[Image:1khc.png|left|200px]]


{{STRUCTURE_1khc|  PDB=1khc  |  SCENE=  }}
==Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b==
 
<StructureSection load='1khc' size='340' side='right'caption='[[1khc]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
===Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b===
== 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>
{{ABSTRACT_PUBMED_11836534}}
</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>
==About this Structure==
<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>
[[1khc]] is a 1 chain structure with sequence from [http://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].  
</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>


==See Also==
==See Also==
*[[DNA methyltransferase|DNA methyltransferase]]
*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:011836534</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[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: Five beta-sheets barrel followed by five-helix bundle]]
[[Category: Transferase]]

Latest revision as of 10:24, 14 February 2024

Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3bCrystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b

Structural highlights

1khc is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).[1] [2] [3] [4] [5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999 Oct 29;99(3):247-57. PMID:10555141
  2. ↑ Gowher H, Jeltsch A. Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases. J Biol Chem. 2002 Jun 7;277(23):20409-14. Epub 2002 Mar 27. PMID:11919202 doi:http://dx.doi.org/10.1074/jbc.M202148200
  3. ↑ Takeshima H, Suetake I, Shimahara H, Ura K, Tate S, Tajima S. Distinct DNA methylation activity of Dnmt3a and Dnmt3b towards naked and nucleosomal DNA. J Biochem. 2006 Mar;139(3):503-15. PMID:16567415 doi:http://dx.doi.org/139/3/503
  4. ↑ Linhart HG, Lin H, Yamada Y, Moran E, Steine EJ, Gokhale S, Lo G, Cantu E, Ehrich M, He T, Meissner A, Jaenisch R. Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing. Genes Dev. 2007 Dec 1;21(23):3110-22. PMID:18056424 doi:http://dx.doi.org/10.1101/gad.1594007
  5. ↑ Kim SH, Park J, Choi MC, Park JH, Kim HP, Lee JH, Oh DY, Im SA, Bang YJ, Kim TY. DNA methyltransferase 3B acts as a co-repressor of the human polycomb protein hPc2 to repress fibroblast growth factor receptor 3 transcription. Int J Biochem Cell Biol. 2008;40(11):2462-71. doi: 10.1016/j.biocel.2008.04.018. , Epub 2008 May 18. PMID:18567530 doi:http://dx.doi.org/10.1016/j.biocel.2008.04.018
  6. ↑ Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat Struct Biol. 2002 Mar;9(3):217-24. PMID:11836534 doi:10.1038/nsb759

1khc, resolution 1.80Å

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