5ff8 - Revision history

OCA at 06:49, 19 July 2023

OCA — Wed, 19 Jul 2023 06:49:05 GMT

←Older revision		Revision as of 06:49, 19 July 2023
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	<StructureSection load='5ff8' size='340' side='right'caption='[[5ff8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5ff8' size='340' side='right'caption='[[5ff8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ff8]] 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=5FF8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FF8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ff8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FF8 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</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]] 1.7Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">TDG ([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=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Thymine~~-~~DNA_glycosylase Thymine~~-~~DNA glycosylase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.2.2.29 3.2.2.29]~~ </~~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=5ff8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff8 OCA], [https://pdbe.org/5ff8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ff8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ff8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff8 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=5ff8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff8 OCA], [~~http~~://pdbe.org/5ff8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ff8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ff8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TDG_HUMAN TDG_HUMAN]] In the DNA of higher eukaryotes, hydrolytic deamination of 5-methylcytosine to thymine leads to the formation of G/T mismatches. This enzyme corrects G/T mispairs to G/C pairs. It is capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and a mispaired thymine. In addition to the G/T, it can remove thymine also from C/T and T/T mispairs in the order G/T >> C/T > T/T. It has no detectable activity on apyrimidinic sites and does not catalyze the removal of thymine from A/T pairs or from single-stranded DNA. It can also remove uracil and 5-bromouracil from mispairs with guanine.	+	[https://www.uniprot.org/uniprot/TDG_HUMAN TDG_HUMAN] In the DNA of higher eukaryotes, hydrolytic deamination of 5-methylcytosine to thymine leads to the formation of G/T mismatches. This enzyme corrects G/T mispairs to G/C pairs. It is capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and a mispaired thymine. In addition to the G/T, it can remove thymine also from C/T and T/T mispairs in the order G/T >> C/T > T/T. It has no detectable activity on apyrimidinic sites and does not catalyze the removal of thymine from A/T pairs or from single-stranded DNA. It can also remove uracil and 5-bromouracil from mispairs with guanine.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thymine-DNA glycosylase~~]]	+	[[Category: Unidentified]]
-	[[Category: Drohat~~, A C~~]]	+	[[Category: Drohat AC]]
-	[[Category: Malik~~, S S~~]]	+	[[Category: Malik SS]]
-	[[Category: Pozharski, E]]	+	[[Category: Pozharski E]]
-	~~[[Category: G-t mismatch-specific thymine dna glycosylase-dna complex]]~~	+
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 11:38, 25 December 2019

OCA — Wed, 25 Dec 2019 11:38:00 GMT

←Older revision		Revision as of 11:38, 25 December 2019
Line 1:		Line 1:

	==TDG enzyme-product complex==		==TDG enzyme-product complex==
-	<StructureSection load='5ff8' size='340' side='right' caption='[[5ff8]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5ff8' size='340' side='right'caption='[[5ff8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ff8]] 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=5FF8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FF8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ff8]] 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=5FF8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FF8 FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5ff8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ff8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Thymine-DNA glycosylase]]		[[Category: Thymine-DNA glycosylase]]
	[[Category: Drohat, A C]]		[[Category: Drohat, A C]]

OCA at 17:14, 15 November 2017

OCA — Wed, 15 Nov 2017 17:14:18 GMT

←Older revision		Revision as of 17:14, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5ff8' size='340' side='right' caption='[[5ff8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5ff8' size='340' side='right' caption='[[5ff8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ff8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FF8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FF8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ff8]] 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=5FF8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FF8 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TDG ([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/Thymine-DNA_glycosylase Thymine-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.29 3.2.2.29] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymine-DNA_glycosylase Thymine-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.29 3.2.2.29] </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=5ff8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff8 OCA], [http://pdbe.org/5ff8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ff8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ff8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff8 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=5ff8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff8 OCA], [http://pdbe.org/5ff8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ff8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ff8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff8 ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Thymine-DNA glycosylase]]		[[Category: Thymine-DNA glycosylase]]
	[[Category: Drohat, A C]]		[[Category: Drohat, A C]]

OCA at 16:47, 3 October 2016

OCA — Mon, 03 Oct 2016 16:47:09 GMT

←Older revision		Revision as of 16:47, 3 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ff8 is ~~ON HOLD until Paper~~ Publication	+	==TDG enzyme-product complex==
		+	<StructureSection load='5ff8' size='340' side='right' caption='[[5ff8]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ff8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FF8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FF8 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymine-DNA_glycosylase Thymine-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.29 3.2.2.29] </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=5ff8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff8 OCA], [http://pdbe.org/5ff8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ff8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ff8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TDG_HUMAN TDG_HUMAN]] In the DNA of higher eukaryotes, hydrolytic deamination of 5-methylcytosine to thymine leads to the formation of G/T mismatches. This enzyme corrects G/T mispairs to G/C pairs. It is capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and a mispaired thymine. In addition to the G/T, it can remove thymine also from C/T and T/T mispairs in the order G/T >> C/T > T/T. It has no detectable activity on apyrimidinic sites and does not catalyze the removal of thymine from A/T pairs or from single-stranded DNA. It can also remove uracil and 5-bromouracil from mispairs with guanine.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thymine DNA Glycosylase (TDG) is a base excision repair enzyme functioning in DNA repair and epigenetic regulation. TDG removes thymine from mutagenic G.T mispairs arising from deamination of 5-methylcytosine (mC), and it processes other deamination-derived lesions including uracil (U). Essential for DNA demethylation, TDG excises 5-formylcytosine and 5-carboxylcytosine, derivatives of mC generated by Tet (ten-eleven translocation) enzymes. Here, we report structural and functional studies of TDG82-308, a new construct containing 29 more N-terminal residues than TDG111-308, the construct used for previous structures of DNA-bound TDG. Crystal structures and NMR experiments demonstrate that most of these N-terminal residues are disordered, for substrate- or product-bound TDG82-308 Nevertheless, G.T substrate affinity and glycosylase activity of TDG82-308 greatly exceeds that of TDG111-308 and is equivalent to full-length TDG. We report the first high-resolution structures of TDG in an enzyme-substrate complex, for G.U bound to TDG82-308 (1.54 A) and TDG111-308 (1.71 A), revealing new enzyme-substrate contacts, direct and water-mediated. We also report a structure of the TDG82-308 product complex (1.70 A). TDG82-308 forms unique enzyme-DNA interactions, supporting its value for structure-function studies. The results advance understanding of how TDG recognizes and removes modified bases from DNA, particularly those resulting from deamination.

-	~~Authors~~: ~~Pozharski, E~~., Malik, ~~S.S.~~, ~~Drohat~~, A.C.	+	Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues.,Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC Nucleic Acids Res. 2016 Aug 31. pii: gkw768. PMID:27580719<ref>PMID:27580719</ref>

-	~~Description~~: ~~TDG enzyme~~-~~product complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Malik, S.S]]	+	<div class="pdbe-citations 5ff8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Thymine-DNA glycosylase]]
		+	[[Category: Drohat, A C]]
		+	[[Category: Malik, S S]]
	[[Category: Pozharski, E]]		[[Category: Pozharski, E]]
-	[[Category: ~~Drohat, A.C~~]]	+	[[Category: G-t mismatch-specific thymine dna glycosylase-dna complex]]
		+	[[Category: Hydrolase-dna complex]]

OCA at 18:11, 13 January 2016

OCA — Wed, 13 Jan 2016 18:11:09 GMT

←Older revision		Revision as of 18:11, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ff8 is ON HOLD	+	The entry 5ff8 is ON HOLD until Paper Publication

	Authors: Pozharski, E., Malik, S.S., Drohat, A.C.		Authors: Pozharski, E., Malik, S.S., Drohat, A.C.

OCA: Protected "5ff8" [edit=sysop:move=sysop]

OCA — Wed, 23 Dec 2015 11:34:53 GMT

Protected "5ff8" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:34, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5ff8 is ON HOLD Authors: Pozharski, E., Malik, S.S., Drohat, A.C. Description: TDG enzyme-product complex Category: Unreleased Structures [[Cat...

OCA — Wed, 23 Dec 2015 11:34:52 GMT

New page: '''Unreleased structure''' The entry 5ff8 is ON HOLD Authors: Pozharski, E., Malik, S.S., Drohat, A.C. Description: TDG enzyme-product complex Category: Unreleased Structures [[Cat...

New page

'''Unreleased structure'''

The entry 5ff8 is ON HOLD

Authors: Pozharski, E., Malik, S.S., Drohat, A.C.

Description: TDG enzyme-product complex
[[Category: Unreleased Structures]]
[[Category: Malik, S.S]]
[[Category: Pozharski, E]]
[[Category: Drohat, A.C]]