3sau - Revision history

OCA at 12:52, 14 March 2024

OCA — Thu, 14 Mar 2024 12:52:13 GMT

←Older revision		Revision as of 12:52, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3sau' size='340' side='right'caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='3sau' size='340' side='right'caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SAU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SAU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.65Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</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"><div style='overflow: auto; max-height: 3em;'>[[3sar\|3sar]]~~, ~~[[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">MUTM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [https://pdbe.org/3sau PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [https://www.ebi.ac.uk/pdbsum/3sau PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sau 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=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [https://pdbe.org/3sau PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [https://www.ebi.ac.uk/pdbsum/3sau PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sau ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]	+	[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.	+
-		+
-	Strandwise translocation of a DNA glycosylase on undamaged DNA.,Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1086-91. Epub 2012 Jan 4. PMID:22219368<ref>PMID:22219368</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3sau" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]		*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Qi, Y]]	+	[[Category: Qi Y]]
-	[[Category: Spong~~, M C~~]]	+	[[Category: Spong MC]]
-	[[Category: Verdine~~, G L]]~~	+	[[Category: Verdine GL]]
-	~~[[Category: Damage search]]~~	+
-	~~[[Category: Disulfide crosslinking]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna glycosylase]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Multifunctional enzyme]]~~	+
-	~~[[Category: Translocation]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 07:49, 29 June 2022

OCA — Wed, 29 Jun 2022 07:49:08 GMT

OCA at 11:38, 17 July 2019

OCA — Wed, 17 Jul 2019 11:38:02 GMT

←Older revision		Revision as of 11:38, 17 July 2019
Line 1:		Line 1:

	==MUTM Interrogation complex 6==		==MUTM Interrogation complex 6==
-	<StructureSection load='3sau' size='340' side='right' caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='3sau' size='340' side='right'caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAU FirstGlance]. <br>
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 3sau" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3sau" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
		+	[[Category: Large Structures]]
	[[Category: Qi, Y]]		[[Category: Qi, Y]]
	[[Category: Spong, M C]]		[[Category: Spong, M C]]

OCA at 09:35, 8 November 2017

OCA — Wed, 08 Nov 2017 09:35:53 GMT

←Older revision		Revision as of 09:35, 8 November 2017
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 3sau" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3sau" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:18, 5 August 2016

OCA — Fri, 05 Aug 2016 22:18:52 GMT

←Older revision		Revision as of 22:18, 5 August 2016
Line 1:		Line 1:
		+
	==MUTM Interrogation complex 6==		==MUTM Interrogation complex 6==
	<StructureSection load='3sau' size='340' side='right' caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='3sau' size='340' side='right' caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sar\|3sar]], [[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sar\|3sar]], [[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ~~Geobacillus stearothermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [http://www.ebi.ac.uk/pdbsum/3sau 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=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [http://pdbe.org/3sau PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [http://www.ebi.ac.uk/pdbsum/3sau PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sau 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 3sau" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geobacillus stearothermophilus~~]]	+	[[Category: Atcc 12980]]
	[[Category: Qi, Y]]		[[Category: Qi, Y]]
	[[Category: Spong, M C]]		[[Category: Spong, M C]]

OCA at 22:23, 25 December 2014

OCA — Thu, 25 Dec 2014 22:23:42 GMT

←Older revision		Revision as of 22:23, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sar\|3sar]], [[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sar\|3sar]], [[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [http://www.ebi.ac.uk/pdbsum/3sau 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=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [http://www.ebi.ac.uk/pdbsum/3sau PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 18:
	Strandwise translocation of a DNA glycosylase on undamaged DNA.,Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1086-91. Epub 2012 Jan 4. PMID:22219368<ref>PMID:22219368</ref>		Strandwise translocation of a DNA glycosylase on undamaged DNA.,Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1086-91. Epub 2012 Jan 4. PMID:22219368<ref>PMID:22219368</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
		+
		+	==See Also==
		+	*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Qi, Y.]]	+	[[Category: Qi, Y]]
-	[[Category: Spong, M C.]]	+	[[Category: Spong, M C]]
-	[[Category: Verdine, G L.]]	+	[[Category: Verdine, G L]]
	[[Category: Damage search]]		[[Category: Damage search]]
	[[Category: Disulfide crosslinking]]		[[Category: Disulfide crosslinking]]

OCA at 05:19, 5 June 2014

OCA — Thu, 05 Jun 2014 05:19:24 GMT

←Older revision		Revision as of 05:19, 5 June 2014
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-	[[~~Image:~~3sau.~~png~~\|~~left~~\|~~200px~~]]	+	==MUTM Interrogation complex 6==
		+	<StructureSection load='3sau' size='340' side='right' caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SAU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sar\|3sar]], [[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [http://www.ebi.ac.uk/pdbsum/3sau PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

-	~~<!--~~	+	Strandwise translocation of a DNA glycosylase on undamaged DNA.,Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1086-91. Epub 2012 Jan 4. PMID:22219368<ref>PMID:22219368</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3sau"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_3sau\| PDB=3sau \| SCENE= }}~~	+

-	~~===MUTM Interrogation complex 6===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_22219368}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22219368 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22219368}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3sau]] is a 3 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022219368<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Qi, Y.]]		[[Category: Qi, Y.]]

OCA at 08:44, 29 February 2012

OCA — Wed, 29 Feb 2012 08:44:38 GMT

←Older revision		Revision as of 08:44, 29 February 2012
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	===MUTM Interrogation complex 6===		===MUTM Interrogation complex 6===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22219368}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22219368 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22219368}}

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

OCA at 06:36, 22 February 2012

OCA — Wed, 22 Feb 2012 06:36:06 GMT

←Older revision		Revision as of 06:36, 22 February 2012
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	==About this Structure==		==About this Structure==
	[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA].		[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022219368</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Qi, Y.]]		[[Category: Qi, Y.]]

OCA at 06:27, 11 January 2012

OCA — Wed, 11 Jan 2012 06:27:10 GMT

←Older revision		Revision as of 06:27, 11 January 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:3sau.png\|left\|200px]]

-	The ~~entry 3sau~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3sau", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3sau\| PDB=3sau \| SCENE= }}

-	~~Authors: Spong, M.C., Qi, Y., Verdine, G.L.~~	+	===MUTM Interrogation complex 6===

-	~~Description~~: ~~MUTM Interrogation~~ complex 6	+
		+	==About this Structure==
		+	[[3sau]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA].
		+	[[Category: Geobacillus stearothermophilus]]
		+	[[Category: Qi, Y.]]
		+	[[Category: Spong, M C.]]
		+	[[Category: Verdine, G L.]]
		+	[[Category: Damage search]]
		+	[[Category: Disulfide crosslinking]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna glycosylase]]
		+	[[Category: Dna repair]]
		+	[[Category: Dna-binding]]
		+	[[Category: Glycosidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Lyase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Multifunctional enzyme]]
		+	[[Category: Translocation]]
		+	[[Category: Zinc-finger]]

←Older revision		Revision as of 07:49, 29 June 2022
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	<StructureSection load='3sau' size='340' side='right'caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='3sau' size='340' side='right'caption='[[3sau]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3SAU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sau]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SAU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SAU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TX2:5-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE'>TX2</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sar\|3sar]], [[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sar\|3sar]], [[3sas\|3sas]], [[3sat\|3sat]], [[3sav\|3sav]], [[3saw\|3saw]], [[3sbj\|3sbj]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTM ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [~~http~~://pdbe.org/3sau PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3sau PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3sau 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=3sau FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sau OCA], [https://pdbe.org/3sau PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sau RCSB], [https://www.ebi.ac.uk/pdbsum/3sau PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sau ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]	+	[[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==