3pt6

From Proteopedia

(Difference between revisions)

Revision as of 20:34, 4 August 2016

Crystal structure of mouse DNMT1(650-1602) in complex with DNA

Structural highlights

3pt6 is a 6 chain structure with sequence from Lk3 transgenic mice. The July 2011 RCSB PDB Molecule of the Month feature on DNA Methylases by David Goodsell is 10.2210/rcsb_pdb/mom_2011_7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3pt9, 3pta
Gene:	Dnmt1, Dnmt, Met1, Uim (LK3 transgenic mice)
Activity:	DNA (cytosine-5-)-methyltransferase, with EC number 2.1.1.37
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DNMT1_MOUSE] Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B 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.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2) and methyltransferase domains bound to DNA containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, thereby preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position, and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, whereby occlusion of unmethylated CpG dinucleotides from de novo methylation ensures that only hemimethylated CpG dinucleotides gain access to the active site.

Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation.,Song J, Rechkoblit O, Bestor TH, Patel DJ Science. 2010 Dec 16. PMID:21163962^[4]

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

References

↑ Howell CY, Bestor TH, Ding F, Latham KE, Mertineit C, Trasler JM, Chaillet JR. Genomic imprinting disrupted by a maternal effect mutation in the Dnmt1 gene. Cell. 2001 Mar 23;104(6):829-38. PMID:11290321
↑ Easwaran HP, Schermelleh L, Leonhardt H, Cardoso MC. Replication-independent chromatin loading of Dnmt1 during G2 and M phases. EMBO Rep. 2004 Dec;5(12):1181-6. PMID:15550930 doi:http://dx.doi.org/10.1038/sj.embor.7400295
↑ Schermelleh L, Haemmer A, Spada F, Rosing N, Meilinger D, Rothbauer U, Cardoso MC, Leonhardt H. Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation. Nucleic Acids Res. 2007;35(13):4301-12. Epub 2007 Jun 18. PMID:17576694 doi:http://dx.doi.org/10.1093/nar/gkm432
↑ Song J, Rechkoblit O, Bestor TH, Patel DJ. Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation. Science. 2010 Dec 16. PMID:21163962 doi:10.1126/science.1195380

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3pt6"

@@ Line 1: / Line 1: @@
 ==Crystal structure of mouse DNMT1(650-1602) in complex with DNA==
 <StructureSection load='3pt6' size='340' side='right' caption='[[3pt6]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3pt6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. The July 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Methylases''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_7 10.2210/rcsb_pdb/mom_2011_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PT6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PT6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3pt6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. The July 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Methylases''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_7 10.2210/rcsb_pdb/mom_2011_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PT6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PT6 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3pt9|3pt9]], [[3pta|3pta]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dnmt1, Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dnmt1, Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></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=3pt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pt6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pt6 PDBsum]</span></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=3pt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pt6 OCA], [http://pdbe.org/3pt6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pt6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pt6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pt6 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3pt6" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 27: / Line 29: @@
 </StructureSection>
 [[Category: DNA Methylases]]
-[[Category: Mus musculus]]
+[[Category: Lk3 transgenic mice]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Patel, D J]]

3pt6

From Proteopedia

Revision as of 20:34, 4 August 2016

Crystal structure of mouse DNMT1(650-1602) in complex with DNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox