3vxx: Difference between revisions

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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===
-{{ABSTRACT_PUBMED_23316048}}
-==Function==
+==Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence==
-[[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.
+<StructureSection load='3vxx' size='340' side='right'caption='[[3vxx]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3vxx]] is a 3 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=3VXX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VXX 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]] 2.204&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=3vxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxx OCA], [https://pdbe.org/3vxx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vxx RCSB], [https://www.ebi.ac.uk/pdbsum/3vxx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vxx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://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.
+<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.
-==About this Structure==
+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>
-[[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].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:023316048</ref><references group="xtra"/><references/>
+</div>
+<div class="pdbe-citations 3vxx" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[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: Methyl cpg binding domain]]
-[[Category: Protein-dna complex]]
-[[Category: Versatile base recognition]]