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{{STRUCTURE_3vxx|  PDB=3vxx  |  SCENE=  }}
==Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence==
===Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence===
<StructureSection load='3vxx' size='340' side='right' caption='[[3vxx]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
{{ABSTRACT_PUBMED_23316048}}
== Structural highlights ==
<table><tr><td colspan='2'>[[3vxx]] is a 3 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=3VXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VXX FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vxv|3vxv]], [[3vyb|3vyb]], [[3vyq|3vyq]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mbd4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</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=3vxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vxx RCSB], [http://www.ebi.ac.uk/pdbsum/3vxx PDBsum]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The methyl-CpG binding domain (MBD) protein MBD4 participates in DNA repair as a glycosylase that excises mismatched thymine bases in CpG sites and also functions in transcriptional repression. Unlike other MBD proteins, MBD4 recognizes not only methylated CpG dinucleotides ((5m)CG/(5m)CG) but also T/G mismatched sites generated by spontaneous deamination of 5-methylcytosine ((5m)CG/TG). The glycosylase activity of MBD4 is also implicated in active DNA demethylation initiated by the deaminase-catalyzed conversion of 5-methylcytosine to thymine. Here, we report the crystal structures of the MBD of MBD4 (MBDMBD4) complexed with (5m)CG/(5m)CG and (5m)CG/TG. The crystal structures show that the DNA interface of MBD4 has flexible structural features and harbors an extensive water network that supports its dual base specificities. Combined with the results of biochemical analyses, the crystal structure of MBD4 bound to 5-hydroxymethylcytosine further demonstrates that MBDMBD4 is able to recognize a wide range of 5-methylcytosine modifications through the unique water network. The versatile base recognition ability of MBDMBD4 implies multifunctional roles for MBD4 in the regulation of dynamic DNA methylation patterns coupled with deamination and/or oxidation of 5-methylcytosine.


==Function==
Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.,Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M J Biol Chem. 2013 Mar 1;288(9):6351-62. doi: 10.1074/jbc.M112.431098. Epub 2013, Jan 10. PMID:23316048<ref>PMID:23316048</ref>
[[http://www.uniprot.org/uniprot/MBD4_MOUSE MBD4_MOUSE]] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.  


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[3vxx]] is a 3 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=3VXX OCA].
</div>


==Reference==
==See Also==
<ref group="xtra">PMID:023316048</ref><references group="xtra"/><references/>
*[[Methyl CpG binding protein|Methyl CpG binding protein]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Arita, K.]]
[[Category: Arita, K]]
[[Category: Ariyoshi, M.]]
[[Category: Ariyoshi, M]]
[[Category: Kato, T.]]
[[Category: Kato, T]]
[[Category: Kinoshita, M.]]
[[Category: Kinoshita, M]]
[[Category: Otani, J.]]
[[Category: Otani, J]]
[[Category: Shirakawa, M.]]
[[Category: Shirakawa, M]]
[[Category: Hydrolase-dna complex]]
[[Category: Hydrolase-dna complex]]
[[Category: Methyl cpg binding domain]]
[[Category: Methyl cpg binding domain]]
[[Category: Protein-dna complex]]
[[Category: Protein-dna complex]]
[[Category: Versatile base recognition]]
[[Category: Versatile base recognition]]

Revision as of 10:27, 21 December 2014

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequenceCrystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence

Structural highlights

3vxx is a 3 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:
Gene:Mbd4 (Mus musculus)
Resources:FirstGlance, OCA, RCSB, PDBsum

Publication Abstract from PubMed

The methyl-CpG binding domain (MBD) protein MBD4 participates in DNA repair as a glycosylase that excises mismatched thymine bases in CpG sites and also functions in transcriptional repression. Unlike other MBD proteins, MBD4 recognizes not only methylated CpG dinucleotides ((5m)CG/(5m)CG) but also T/G mismatched sites generated by spontaneous deamination of 5-methylcytosine ((5m)CG/TG). The glycosylase activity of MBD4 is also implicated in active DNA demethylation initiated by the deaminase-catalyzed conversion of 5-methylcytosine to thymine. Here, we report the crystal structures of the MBD of MBD4 (MBDMBD4) complexed with (5m)CG/(5m)CG and (5m)CG/TG. The crystal structures show that the DNA interface of MBD4 has flexible structural features and harbors an extensive water network that supports its dual base specificities. Combined with the results of biochemical analyses, the crystal structure of MBD4 bound to 5-hydroxymethylcytosine further demonstrates that MBDMBD4 is able to recognize a wide range of 5-methylcytosine modifications through the unique water network. The versatile base recognition ability of MBDMBD4 implies multifunctional roles for MBD4 in the regulation of dynamic DNA methylation patterns coupled with deamination and/or oxidation of 5-methylcytosine.

Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.,Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M J Biol Chem. 2013 Mar 1;288(9):6351-62. doi: 10.1074/jbc.M112.431098. Epub 2013, Jan 10. PMID:23316048[1]

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

See Also

References

  1. ↑ Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M. Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4. J Biol Chem. 2013 Mar 1;288(9):6351-62. doi: 10.1074/jbc.M112.431098. Epub 2013, Jan 10. PMID:23316048 doi:10.1074/jbc.M112.431098

3vxx, resolution 2.20Å

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