5ydr - Revision history

OCA at 08:27, 22 November 2023

OCA — Wed, 22 Nov 2023 08:27:22 GMT

←Older revision		Revision as of 08:27, 22 November 2023
Line 1:		Line 1:

	==Structure of DNMT1 RFTS domain in complex with ubiquitin==		==Structure of DNMT1 RFTS domain in complex with ubiquitin==
-	<StructureSection load='5ydr' size='340' side='right' caption='[[5ydr]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5ydr' size='340' side='right'caption='[[5ydr]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ydr]] 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=5YDR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ydr]] 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=5YDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YDR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.003Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), DNMT1, AIM, CXXC9, DNMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5ydr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydr OCA], [https://pdbe.org/5ydr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ydr RCSB], [https://www.ebi.ac.uk/pdbsum/5ydr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydr 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=5ydr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydr OCA], [~~http~~://pdbe.org/5ydr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ydr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ydr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydr ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/DNMT1_HUMAN DNMT1_HUMAN]] Defects in DNMT1 are the cause of hereditary sensory neuropathy type 1E (HSN1E) [MIM:[http://omim.org/entry/614116 614116]]. A neurodegenerative disorder characterized by adult onset of progressive peripheral sensory loss associated with progressive hearing impairment and early-onset dementia.<ref>PMID:21532572</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~DNMT1_HUMAN DNMT1_HUMAN~~]~~] 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:~~16357870</ref> <ref>PMID:18754681~~</ref> <ref>PMID:~~18413740~~</ref>	+	[https://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ydr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ydr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA methyltransferase 3D structures\|DNA methyltransferase 3D structures]]
		+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Qian, C~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Dna methylation]]~~	+	[[Category: Qian C]]
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Protein binding-transferase complex~~]]	+

OCA at 06:41, 18 April 2018

OCA — Wed, 18 Apr 2018 06:41:42 GMT

←Older revision		Revision as of 06:41, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='5ydr' size='340' side='right' caption='[[5ydr]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5ydr' size='340' side='right' caption='[[5ydr]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ydr]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ydr]] 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=5YDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=PO4:PHOSPHATE+ION'>PO4</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">UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DNMT1, AIM, CXXC9, DNMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ydr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydr OCA], [http://pdbe.org/5ydr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydr RCSB], [http://www.ebi.ac.uk/pdbsum/5ydr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydr 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=5ydr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydr OCA], [http://pdbe.org/5ydr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydr RCSB], [http://www.ebi.ac.uk/pdbsum/5ydr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydr ProSAT]</span></td></tr>
Line 12:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DNMT1_HUMAN DNMT1_HUMAN]] 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:16357870</ref> <ref>PMID:18754681</ref> <ref>PMID:18413740</ref>		[[http://www.uniprot.org/uniprot/DNMT1_HUMAN DNMT1_HUMAN]] 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:16357870</ref> <ref>PMID:18754681</ref> <ref>PMID:18413740</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	UHRF1 plays multiple roles in regulating DNMT1-mediated DNA methylation maintenance during DNA replication. The UHRF1 C-terminal RING finger functions as an ubiquitin E3 ligase to establish histone H3 ubiquitination at Lys18 and/or Lys23, which is subsequently recognized by DNMT1 to promote its localization onto replication foci. Here, we present the crystal structure of DNMT1 RFTS domain in complex with ubiquitin and highlight a unique ubiquitin binding mode for the RFTS domain. We provide evidence that UHRF1 N-terminal ubiquitin-like domain (UBL) also binds directly to DNMT1. Despite sharing a high degree of structural similarity, UHRF1 UBL and ubiquitin bind to DNMT1 in a very distinct fashion and exert different impacts on DNMT1 enzymatic activity. We further show that the UHRF1 UBL-mediated interaction between UHRF1 and DNMT1, and the binding of DNMT1 to ubiquitinated histone H3 that is catalyzed by UHRF1 RING domain are critical for the proper subnuclear localization of DNMT1 and maintenance of DNA methylation. Collectively, our study adds another layer of complexity to the regulatory mechanism of DNMT1 activation by UHRF1 and supports that individual domains of UHRF1 participate and act in concert to maintain DNA methylation patterns.
		+
		+	Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation.,Li T, Wang L, Du Y, Xie S, Yang X, Lian F, Zhou Z, Qian C Nucleic Acids Res. 2018 Apr 6;46(6):3218-3231. doi: 10.1093/nar/gky104. PMID:29471350<ref>PMID:29471350</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ydr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Qian, C]]		[[Category: Qian, C]]
	[[Category: Dna methylation]]		[[Category: Dna methylation]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Protein binding-transferase complex]]		[[Category: Protein binding-transferase complex]]

OCA at 07:21, 22 February 2018

OCA — Thu, 22 Feb 2018 07:21:30 GMT

←Older revision		Revision as of 07:21, 22 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ydr is ~~ON HOLD~~	+	==Structure of DNMT1 RFTS domain in complex with ubiquitin==
-		+	<StructureSection load='5ydr' size='340' side='right' caption='[[5ydr]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Qian~~, C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ydr]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDR FirstGlance]. <br>
-	~~Description~~: ~~DNA methylation maintenance complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5ydr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydr OCA], [http://pdbe.org/5ydr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydr RCSB], [http://www.ebi.ac.uk/pdbsum/5ydr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydr ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DNMT1_HUMAN DNMT1_HUMAN]] Defects in DNMT1 are the cause of hereditary sensory neuropathy type 1E (HSN1E) [MIM:[http://omim.org/entry/614116 614116]]. A neurodegenerative disorder characterized by adult onset of progressive peripheral sensory loss associated with progressive hearing impairment and early-onset dementia.<ref>PMID:21532572</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNMT1_HUMAN DNMT1_HUMAN]] 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:16357870</ref> <ref>PMID:18754681</ref> <ref>PMID:18413740</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Qian, C]]		[[Category: Qian, C]]
		+	[[Category: Dna methylation]]
		+	[[Category: Protein binding]]
		+	[[Category: Protein binding-transferase complex]]

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

OCA — Wed, 27 Sep 2017 16:26:55 GMT

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

←Older revision

Revision as of 16:26, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ydr is ON HOLD Authors: Qian, C. Description: DNA methylation maintenance complex Category: Unreleased Structures Category: Qian, C

OCA — Wed, 27 Sep 2017 16:26:54 GMT

New page: '''Unreleased structure''' The entry 5ydr is ON HOLD Authors: Qian, C. Description: DNA methylation maintenance complex Category: Unreleased Structures Category: Qian, C

New page

'''Unreleased structure'''

The entry 5ydr is ON HOLD

Authors: Qian, C.

Description: DNA methylation maintenance complex
[[Category: Unreleased Structures]]
[[Category: Qian, C]]