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6d1t

From Proteopedia

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Complex of MBD1-MBD and methylated DNA

Structural highlights

6d1t is a 3 chain structure with sequence from Homo sapiens and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MBD1_HUMAN Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

References

↑ Cross SH, Meehan RR, Nan X, Bird A. A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins. Nat Genet. 1997 Jul;16(3):256-9. PMID:9207790 doi:http://dx.doi.org/10.1038/ng0797-256
↑ Fujita N, Takebayashi S, Okumura K, Kudo S, Chiba T, Saya H, Nakao M. Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms. Mol Cell Biol. 1999 Sep;19(9):6415-26. PMID:10454587
↑ Hendrich B, Bird A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol. 1998 Nov;18(11):6538-47. PMID:9774669
↑ Ng HH, Jeppesen P, Bird A. Active repression of methylated genes by the chromosomal protein MBD1. Mol Cell Biol. 2000 Feb;20(4):1394-406. PMID:10648624
↑ Fujita N, Watanabe S, Ichimura T, Tsuruzoe S, Shinkai Y, Tachibana M, Chiba T, Nakao M. Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression. J Biol Chem. 2003 Jun 27;278(26):24132-8. Epub 2003 Apr 23. PMID:12711603 doi:http://dx.doi.org/10.1074/jbc.M302283200
↑ Fujita N, Watanabe S, Ichimura T, Ohkuma Y, Chiba T, Saya H, Nakao M. MCAF mediates MBD1-dependent transcriptional repression. Mol Cell Biol. 2003 Apr;23(8):2834-43. PMID:12665582
↑ Reese BE, Bachman KE, Baylin SB, Rountree MR. The methyl-CpG binding protein MBD1 interacts with the p150 subunit of chromatin assembly factor 1. Mol Cell Biol. 2003 May;23(9):3226-36. PMID:12697822
↑ Ghoshal K, Majumder S, Datta J, Motiwala T, Bai S, Sharma SM, Frankel W, Jacob ST. Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression. J Biol Chem. 2004 Feb 20;279(8):6783-93. Epub 2003 Nov 10. PMID:14610093 doi:http://dx.doi.org/10.1074/jbc.M309393200
↑ Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell. 2004 Aug 27;15(4):595-605. PMID:15327775 doi:http://dx.doi.org/10.1016/j.molcel.2004.06.043
↑ Watanabe S, Ichimura T, Fujita N, Tsuruzoe S, Ohki I, Shirakawa M, Kawasuji M, Nakao M. Methylated DNA-binding domain 1 and methylpurine-DNA glycosylase link transcriptional repression and DNA repair in chromatin. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12859-64. Epub 2003 Oct 10. PMID:14555760 doi:http://dx.doi.org/10.1073/pnas.2131819100

1 Structural highlights
2 Function
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6d1t"

@@ Line 1: / Line 1: @@
 ==Complex of MBD1-MBD and methylated DNA==
-<StructureSection load='6d1t' size='340' side='right' caption='[[6d1t]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+<StructureSection load='6d1t' size='340' side='right'caption='[[6d1t]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6d1t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D1T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6d1t]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D1T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</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='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=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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6d1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1t OCA], [http://pdbe.org/6d1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d1t RCSB], [http://www.ebi.ac.uk/pdbsum/6d1t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1t ProSAT]</span></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=6d1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1t OCA], [https://pdbe.org/6d1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d1t RCSB], [https://www.ebi.ac.uk/pdbsum/6d1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN]] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>
+[https://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>
+==See Also==
+*[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arrowsmith, C H]]
+[[Category: Homo sapiens]]
-[[Category: Bountra, C]]
+[[Category: Large Structures]]
-[[Category: Edwards, A M]]
+[[Category: Synthetic construct]]
-[[Category: Liu, K]]
+[[Category: Arrowsmith CH]]
-[[Category: Min, J]]
+[[Category: Bountra C]]
-[[Category: Structural genomic]]
+[[Category: Edwards AM]]
-[[Category: Tempel, W]]
+[[Category: Liu K]]
-[[Category: Xu, C]]
+[[Category: Min J]]
-[[Category: Dna binding protein-dna complex]]
+[[Category: Tempel W]]
-[[Category: Dna-methylation]]
+[[Category: Xu C]]
-[[Category: Mbd]]
-[[Category: Sgc]]

6d1t

From Proteopedia

Current revision

Complex of MBD1-MBD and methylated DNA

Structural highlights

Function

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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