4e9f - Revision history

OCA at 14:56, 14 March 2024

2024-03-14T14:56:04Z

← Older revision		Revision as of 14:56, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e9f]] 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=4E9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E9F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e9f]] 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=4E9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E9F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.79Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [https://pdbe.org/4e9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [https://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f 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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [https://pdbe.org/4e9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [https://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/MBD4_HUMAN MBD4_HUMAN]] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.<ref>PMID:10097147</ref> <ref>PMID:10930409</ref>		[https://www.uniprot.org/uniprot/MBD4_HUMAN MBD4_HUMAN] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.<ref>PMID:10097147</ref> <ref>PMID:10930409</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Active DNA demethylation in mammals occurs via hydroxylation of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation family of proteins (TETs). 5hmC residues in DNA can be further oxidized by TETs to 5-carboxylcytosines and/or deaminated by the Activation Induced Deaminase/Apolipoprotein B mRNA-editing enzyme complex family proteins to 5-hydromethyluracil (5hmU). Excision and replacement of these intermediates is initiated by DNA glycosylases such as thymine-DNA glycosylase (TDG), methyl-binding domain protein 4 (MBD4) and single-strand specific monofunctional uracil-DNA glycosylase 1 in the base excision repair pathway. Here, we report detailed biochemical and structural characterization of human MBD4 which contains mismatch-specific TDG activity. Full-length as well as catalytic domain (residues 426-580) of human MBD4 (MBD4(cat)) can remove 5hmU when opposite to G with good efficiency. Here, we also report six crystal structures of human MBD4(cat): an unliganded form and five binary complexes with duplex DNA containing a TG, 5hmUG or AP*G (apurinic/apyrimidinic) mismatch at the target base pair. These structures reveal that MBD4(cat) uses a base flipping mechanism to specifically recognize thymine and 5hmU. The recognition mechanism of flipped-out 5hmU bases in MBD4(cat) active site supports the potential role of MBD4, together with TDG, in maintenance of genome stability and active DNA demethylation in mammals.

	Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.,Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA Nucleic Acids Res. 2012 Jul 30. PMID:22848106<ref>PMID:22848106</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e9f" style="background-color:#fffaf0;"></div~~>

	==See Also==		==See Also==

OCA at 06:58, 28 September 2022

2022-09-28T06:58:35Z

← Older revision		Revision as of 06:58, 28 September 2022
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	<StructureSection load='4e9f' size='340' side='right'caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='4e9f' size='340' side='right'caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e9f]] 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=4E9F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E9F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e9f]] 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=4E9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E9F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	~~<tr~~ id~~='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class~~="~~sblockDat~~"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [https://pdbe.org/4e9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [https://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f ProSAT]</span></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[4e9e\|4e9e]]~~, ~~[[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>~~
	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</~~b></td><td class="sblockDat"~~>~~MBD4, MED1 ([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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [~~http~~://pdbe.org/4e9f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/MBD4_HUMAN MBD4_HUMAN]] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.<ref>PMID:10097147</ref> <ref>PMID:10930409</ref>		[[https://www.uniprot.org/uniprot/MBD4_HUMAN MBD4_HUMAN]] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.<ref>PMID:10097147</ref> <ref>PMID:10930409</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==
	*[[Methyl CpG binding protein\|Methyl CpG binding protein]]		*[[Methyl CpG binding protein 3D structures\|Methyl CpG binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Morera, S]]		[[Category: Morera S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux A]]
	~~[[Category: Hhh dna glycosylase family]]~~
	~~[[Category: Hydrolase-dna complex~~]]

OCA at 07:56, 27 March 2019

2019-03-27T07:56:49Z

← Older revision		Revision as of 07:56, 27 March 2019
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	==Structure of the glycosylase domain of MBD4 bound to AP site containing DNA==		==Structure of the glycosylase domain of MBD4 bound to AP site containing DNA==
	<StructureSection load='4e9f' size='340' side='right' caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='4e9f' size='340' side='right'caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e9f]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E9F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e9f]] 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=4E9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E9F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e9e\|4e9e]], [[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e9e\|4e9e]], [[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MBD4, MED1 ([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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://pdbe.org/4e9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f 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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://pdbe.org/4e9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]
	[[Category: Hhh dna glycosylase family]]		[[Category: Hhh dna glycosylase family]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]

OCA at 09:31, 2 January 2017

2017-01-02T09:31:23Z

← Older revision		Revision as of 09:31, 2 January 2017
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	==~~Stucture~~ of the glycosylase domain of MBD4 bound to AP site containing DNA==		==Structure of the glycosylase domain of MBD4 bound to AP site containing DNA==
	<StructureSection load='4e9f' size='340' side='right' caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='4e9f' size='340' side='right' caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e9f]] 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=4E9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E9F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e9f]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E9F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e9e\|4e9e]], [[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e9e\|4e9e]], [[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MBD4, MED1 ([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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://pdbe.org/4e9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f 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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://pdbe.org/4e9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f ProSAT]</span></td></tr>
	</table>		</table>
Line 28:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Human]]~~
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]
	[[Category: Hhh dna glycosylase family]]		[[Category: Hhh dna glycosylase family]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]

OCA at 03:18, 5 August 2016

2016-08-05T03:18:35Z

← Older revision		Revision as of 03:18, 5 August 2016
Line 1:		Line 1:

	==Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA==		==Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA==
	<StructureSection load='4e9f' size='340' side='right' caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='4e9f' size='340' side='right' caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e9f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E9F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e9f]] 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=4E9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E9F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e9e\|4e9e]], [[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e9e\|4e9e]], [[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MBD4, MED1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MBD4, MED1 ([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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f 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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://pdbe.org/4e9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e9f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4e9f" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]
	[[Category: Hhh dna glycosylase family]]		[[Category: Hhh dna glycosylase family]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]

OCA at 15:27, 25 December 2014

2014-12-25T15:27:06Z

← Older revision		Revision as of 15:27, 25 December 2014
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	<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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f 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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/MBD4_HUMAN MBD4_HUMAN]] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.<ref>PMID:10097147</ref> <ref>PMID:10930409</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 15:39, 9 December 2014

2014-12-09T15:39:22Z

← Older revision		Revision as of 15:39, 9 December 2014
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	[[~~Image~~:~~4e9f~~.~~png~~\|~~left~~\|~~200px~~]]		==Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA==
			<StructureSection load='4e9f' size='340' side='right' caption='[[4e9f]], [[Resolution\|resolution]] 1.79Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e9f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E9F FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e9e\|4e9e]], [[4e9g\|4e9g]], [[4e9h\|4e9h]], [[4ea4\|4ea4]], [[4eab\|4eab]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MBD4, MED1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=4e9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e9f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e9f RCSB], [http://www.ebi.ac.uk/pdbsum/4e9f PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Active DNA demethylation in mammals occurs via hydroxylation of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation family of proteins (TETs). 5hmC residues in DNA can be further oxidized by TETs to 5-carboxylcytosines and/or deaminated by the Activation Induced Deaminase/Apolipoprotein B mRNA-editing enzyme complex family proteins to 5-hydromethyluracil (5hmU). Excision and replacement of these intermediates is initiated by DNA glycosylases such as thymine-DNA glycosylase (TDG), methyl-binding domain protein 4 (MBD4) and single-strand specific monofunctional uracil-DNA glycosylase 1 in the base excision repair pathway. Here, we report detailed biochemical and structural characterization of human MBD4 which contains mismatch-specific TDG activity. Full-length as well as catalytic domain (residues 426-580) of human MBD4 (MBD4(cat)) can remove 5hmU when opposite to G with good efficiency. Here, we also report six crystal structures of human MBD4(cat): an unliganded form and five binary complexes with duplex DNA containing a TG, 5hmUG or AP*G (apurinic/apyrimidinic) mismatch at the target base pair. These structures reveal that MBD4(cat) uses a base flipping mechanism to specifically recognize thymine and 5hmU. The recognition mechanism of flipped-out 5hmU bases in MBD4(cat) active site supports the potential role of MBD4, together with TDG, in maintenance of genome stability and active DNA demethylation in mammals.

	~~{{STRUCTURE_4e9f\| PDB=4e9f \| SCENE= }}~~		Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.,Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA Nucleic Acids Res. 2012 Jul 30. PMID:22848106<ref>PMID:22848106</ref>

	~~===Stucture~~ of the ~~glycosylase domain~~ of ~~MBD4 bound to AP site containing DNA===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

			==See Also==
	==~~About this Structure~~==		*[[Methyl CpG binding protein\|Methyl CpG binding protein]]
	[[~~4e9f~~]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E9F OCA].		== References ==
			<references/>
	==~~Reference~~==		__TOC__
	<~~ref group="xtra">PMID:022848106<~~/~~ref~~><~~references group="xtra"~~/>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Morera, S.]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A.]]		[[Category: Vigouroux, A]]
	[[Category: Hhh dna glycosylase family]]		[[Category: Hhh dna glycosylase family]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]

OCA at 14:13, 8 November 2012

2012-11-08T14:13:00Z

← Older revision		Revision as of 14:13, 8 November 2012
Line 1:		Line 1:
	[[Image:4e9f.~~jpg~~\|left\|200px]]		[[Image:4e9f.png\|left\|200px]]

	{{STRUCTURE_4e9f\| PDB=4e9f \| SCENE= }}		{{STRUCTURE_4e9f\| PDB=4e9f \| SCENE= }}
Line 5:		Line 5:
	===Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA===		===Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA===

	~~{{ABSTRACT_PUBMED_22848106}}~~

	==About this Structure==		==About this Structure==

OCA at 05:18, 8 August 2012

2012-08-08T05:18:37Z

← Older revision		Revision as of 05:18, 8 August 2012
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		[[Image:4e9f.jpg\|left\|200px]]

	~~The entry~~ 4e9f ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4e9f\| PDB=4e9f \| SCENE= }}

	~~Authors: Morera, S., Vigouroux, A.~~		===Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA===

	~~Description~~: ~~Stucture of the~~ glycosylase ~~domain of MBD4 bound to AP site containing DNA~~		{{ABSTRACT_PUBMED_22848106}}

			==About this Structure==
			[[4e9f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E9F OCA].

			==Reference==
			<ref group="xtra">PMID:022848106</ref><references group="xtra"/>
			[[Category: Homo sapiens]]
			[[Category: Morera, S.]]
			[[Category: Vigouroux, A.]]
			[[Category: Hhh dna glycosylase family]]
			[[Category: Hydrolase-dna complex]]

OCA at 06:39, 11 April 2012

2012-04-11T06:39:51Z

← Older revision		Revision as of 06:39, 11 April 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e9f is ON HOLD		The entry 4e9f is ON HOLD until Paper Publication

	Authors: ~~morera~~, s, ~~vigouroux~~, a		Authors: Morera, S., Vigouroux, A.

	Description: Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA		Description: Stucture of the glycosylase domain of MBD4 bound to AP site containing DNA