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| | ==Crystal structure of Kaiso zinc finger DNA binding protein in complex with methylated CpG site DNA== | | ==Crystal structure of Kaiso zinc finger DNA binding protein in complex with methylated CpG site DNA== |
| - | <StructureSection load='4f6n' size='340' side='right' caption='[[4f6n]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='4f6n' size='340' side='right'caption='[[4f6n]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4f6n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F6N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F6N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4f6n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F6N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F6N FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4f6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f6n OCA], [https://pdbe.org/4f6n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f6n RCSB], [https://www.ebi.ac.uk/pdbsum/4f6n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f6n ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f6m|4f6m]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ZBTB33, KAISO, ZNF348 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4f6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f6n OCA], [http://pdbe.org/4f6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f6n RCSB], [http://www.ebi.ac.uk/pdbsum/4f6n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f6n ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KAISO_HUMAN KAISO_HUMAN]] Transcriptional regulator with bimodal DNA-binding specificity. Binds to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' and also binds to the non-methylated consensus sequence 5'-CTGCNA-3'. Recruits the N-CoR repressor complex to promote histone deacetylation and the formation of repressive chromatin structures in target gene promoters. May contribute to the repression of target genes of the Wnt signaling pathway. May also activate transcription of a subset of target genes by the recruitment of CTNND2.<ref>PMID:11445535</ref> <ref>PMID:14527417</ref> <ref>PMID:15548582</ref> <ref>PMID:15817151</ref> | + | [https://www.uniprot.org/uniprot/KAISO_HUMAN KAISO_HUMAN] Transcriptional regulator with bimodal DNA-binding specificity. Binds to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' and also binds to the non-methylated consensus sequence 5'-CTGCNA-3'. Recruits the N-CoR repressor complex to promote histone deacetylation and the formation of repressive chromatin structures in target gene promoters. May contribute to the repression of target genes of the Wnt signaling pathway. May also activate transcription of a subset of target genes by the recruitment of CTNND2.<ref>PMID:11445535</ref> <ref>PMID:14527417</ref> <ref>PMID:15548582</ref> <ref>PMID:15817151</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Buck-Koehntop, B A]] | + | [[Category: Large Structures]] |
| - | [[Category: Dyson, H J]] | + | [[Category: Buck-Koehntop BA]] |
| - | [[Category: Ekiert, D C]] | + | [[Category: Dyson HJ]] |
| - | [[Category: Martinez-Yamout, M A]] | + | [[Category: Ekiert DC]] |
| - | [[Category: Stanfield, R L]] | + | [[Category: Martinez-Yamout MA]] |
| - | [[Category: Wilson, I A]] | + | [[Category: Stanfield RL]] |
| - | [[Category: Wright, P E]] | + | [[Category: Wilson IA]] |
| - | [[Category: Dna]]
| + | [[Category: Wright PE]] |
| - | [[Category: Dna binding]]
| + | |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Double helix]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Zinc finger]]
| + | |
| Structural highlights
Function
KAISO_HUMAN Transcriptional regulator with bimodal DNA-binding specificity. Binds to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' and also binds to the non-methylated consensus sequence 5'-CTGCNA-3'. Recruits the N-CoR repressor complex to promote histone deacetylation and the formation of repressive chromatin structures in target gene promoters. May contribute to the repression of target genes of the Wnt signaling pathway. May also activate transcription of a subset of target genes by the recruitment of CTNND2.[1] [2] [3] [4]
Publication Abstract from PubMed
Methylation of CpG dinucleotides in DNA is a common epigenetic modification in eukaryotes that plays a central role in maintenance of genome stability, gene silencing, genomic imprinting, development, and disease. Kaiso, a bifunctional Cys(2)His(2) zinc finger protein implicated in tumor-cell proliferation, binds to both methylated CpG (mCpG) sites and a specific nonmethylated DNA motif (TCCTGCNA) and represses transcription by recruiting chromatin remodeling corepression machinery to target genes. Here we report structures of the Kaiso zinc finger DNA-binding domain in complex with its nonmethylated, sequence-specific DNA target (KBS) and with a symmetrically methylated DNA sequence derived from the promoter region of E-cadherin. Recognition of specific bases in the major groove of the core KBS and mCpG sites is accomplished through both classical and methyl CH...O hydrogen-bonding interactions with residues in the first two zinc fingers, whereas residues in the C-terminal extension following the third zinc finger bind in the opposing minor groove and are required for high-affinity binding. The C-terminal region is disordered in the free protein and adopts an ordered structure upon binding to DNA. The structures of these Kaiso complexes provide insights into the mechanism by which a zinc finger protein can recognize mCpG sites as well as a specific, nonmethylated regulatory DNA sequence.
Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.,Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE Proc Natl Acad Sci U S A. 2012 Sep 4. PMID:22949637[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Prokhortchouk A, Hendrich B, Jorgensen H, Ruzov A, Wilm M, Georgiev G, Bird A, Prokhortchouk E. The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev. 2001 Jul 1;15(13):1613-8. PMID:11445535 doi:10.1101/gad.198501
- ↑ Yoon HG, Chan DW, Reynolds AB, Qin J, Wong J. N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso. Mol Cell. 2003 Sep;12(3):723-34. PMID:14527417
- ↑ Ruzov A, Dunican DS, Prokhortchouk A, Pennings S, Stancheva I, Prokhortchouk E, Meehan RR. Kaiso is a genome-wide repressor of transcription that is essential for amphibian development. Development. 2004 Dec;131(24):6185-94. Epub 2004 Nov 17. PMID:15548582 doi:dev.01549
- ↑ Spring CM, Kelly KF, O'Kelly I, Graham M, Crawford HC, Daniel JM. The catenin p120ctn inhibits Kaiso-mediated transcriptional repression of the beta-catenin/TCF target gene matrilysin. Exp Cell Res. 2005 May 1;305(2):253-65. PMID:15817151 doi:S0014-4827(05)00014-5
- ↑ Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE. Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso. Proc Natl Acad Sci U S A. 2012 Sep 4. PMID:22949637 doi:http://dx.doi.org/10.1073/pnas.1213726109
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