5gut - Revision history

OCA at 11:43, 2 August 2023

OCA — Wed, 02 Aug 2023 11:43:14 GMT

←Older revision		Revision as of 11:43, 2 August 2023
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	<StructureSection load='5gut' size='340' side='right'caption='[[5gut]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5gut' size='340' side='right'caption='[[5gut]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gut]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GUT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gut]] is a 1 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=5GUT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GUT 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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.099Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5guv\|5guv~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5gut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gut OCA], [https://pdbe.org/5gut PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gut RCSB], [https://www.ebi.ac.uk/pdbsum/5gut PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gut ProSAT]</span></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=5gut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gut OCA], [~~http~~://pdbe.org/5gut PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gut RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gut PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gut ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DNMT1_MOUSE 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.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>	+	[https://www.uniprot.org/uniprot/DNMT1_MOUSE 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.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[DNA methyltransferase\|DNA methyltransferase]]	+	*[[DNA methyltransferase 3D structures\|DNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Chen~~, S J~~]]	+	[[Category: Chen SJ]]
-	[[Category: Ye, F]]	+	[[Category: Ye F]]
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:31, 13 March 2019

OCA — Wed, 13 Mar 2019 12:31:16 GMT

←Older revision		Revision as of 12:31, 13 March 2019
Line 1:		Line 1:

	==The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A==		==The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A==
-	<StructureSection load='5gut' size='340' side='right' caption='[[5gut]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5gut' size='340' side='right'caption='[[5gut]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gut]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gut]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUT 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=SO4:SULFATE+ION'>SO4</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"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[5guv\|5guv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5guv\|5guv]]</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='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=5gut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gut OCA], [http://pdbe.org/5gut PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gut RCSB], [http://www.ebi.ac.uk/pdbsum/5gut PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gut ProSAT]</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=5gut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gut OCA], [http://pdbe.org/5gut PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gut RCSB], [http://www.ebi.ac.uk/pdbsum/5gut PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gut ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DNMT1_MOUSE 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.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>		[[http://www.uniprot.org/uniprot/DNMT1_MOUSE 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.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA methyltransferase-1 (DNMT1) plays a crucial role in the maintenance of genomic methylation patterns. The crystal structure of DNMT1 was determined in two different states in which the helix that follows the catalytic loop was either kinked (designated helix-kinked) or well folded (designated helix-straight state). Here, we show that the proper structural transition between these two states is required for DNMT1 activity. The mutations of N1248A and R1279D, which did not affect interactions between DNMT1 and substrates or cofactors, allosterically reduced enzymatic activities in vitro by decreasing kcat/ Km for AdoMet. The crystallographic data combined with molecular dynamic (MD) simulations indicated that the N1248A and R1279D mutants bias the catalytic helix to either the kinked or straight conformation. In addition, genetic complementation assays for the two mutants suggested that disturbing the conformational transition reduced DNMT1 activity in cells, which could act additively with existing DNMT inhibitors to decrease DNA methylation. Collectively, our studies provide molecular insights into conformational changes of the catalytic helix, which is essential for DNMT1 catalytic activity, and thus aid in better understanding the relationship between DNMT1 dynamic switching and enzymatic activity.
		+
		+	Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1.,Ye F, Kong X, Zhang H, Liu Y, Shao Z, Jin J, Cai Y, Zhang R, Li L, Zhang YW, Liu YC, Zhang C, Xie W, Yu K, Ding H, Zhao K, Chen S, Jiang H, Baylin SB, Luo C ACS Chem Biol. 2018 Mar 16;13(3):772-781. doi: 10.1021/acschembio.7b00890. Epub, 2018 Feb 8. PMID:29381856<ref>PMID:29381856</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gut" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA methyltransferase\|DNA methyltransferase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Chen, S J]]		[[Category: Chen, S J]]
	[[Category: Ye, F]]		[[Category: Ye, F]]
	[[Category: Mutant]]		[[Category: Mutant]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:38, 13 September 2017

OCA — Wed, 13 Sep 2017 09:38:46 GMT

←Older revision		Revision as of 09:38, 13 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5gut ~~is ON HOLD~~	+	==The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A==
-		+	<StructureSection load='5gut' size='340' side='right' caption='[[5gut]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~: ~~Chen, S~~.J., Ye, F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5gut]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUT FirstGlance]. <br>
-	~~Description~~: ~~The crystal structure of mouse DNMT1~~ (~~731~~-~~1602~~) ~~mutant~~ -~~N1248A~~	+	</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5guv\|5guv]]</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=5gut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gut OCA], [http://pdbe.org/5gut PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gut RCSB], [http://www.ebi.ac.uk/pdbsum/5gut PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gut ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNMT1_MOUSE 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.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, S J]]
	[[Category: Ye, F]]		[[Category: Ye, F]]
-	[[Category: ~~Chen, S.J~~]]	+	[[Category: Mutant]]
		+	[[Category: Transferase]]

OCA: Protected "5gut" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 12:06:39 GMT

Protected "5gut" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:06, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5gut is ON HOLD Authors: Chen, S.J., Ye, F. Description: The crystal structure of mouse DNMT1 (731-1602) mutant -N1248A [[Category: Unreleased Stru...

OCA — Fri, 09 Sep 2016 12:06:38 GMT

New page: '''Unreleased structure''' The entry 5gut is ON HOLD Authors: Chen, S.J., Ye, F. Description: The crystal structure of mouse DNMT1 (731-1602) mutant -N1248A [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 5gut is ON HOLD

Authors: Chen, S.J., Ye, F.

Description: The crystal structure of mouse DNMT1 (731-1602) mutant -N1248A
[[Category: Unreleased Structures]]
[[Category: Ye, F]]
[[Category: Chen, S.J]]