3g4t - Revision history

OCA at 15:36, 1 November 2023

OCA — Wed, 01 Nov 2023 15:36:48 GMT

←Older revision		Revision as of 15:36, 1 November 2023
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	<StructureSection load='3g4t' size='340' side='right'caption='[[3g4t]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='3g4t' size='340' side='right'caption='[[3g4t]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g4t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Metth Metth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g4t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.64Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~UPS~~:~~2-DEOXY-5-O-THIOPHOSPHONOURIDINE~~'>~~UPS~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UPS:2-DEOXY-5-O-THIOPHOSPHONOURIDINE'>UPS</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;'>[[3fzi\|3fzi]]~~, ~~[[3g00\|3g00]], [[3g0a\|3g0a]], [[3g0r\|3g0r]], [[3g1k\|3g1k]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g3y\|3g3y]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=187420 METTH])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [https://pdbe.org/3g4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [https://www.ebi.ac.uk/pdbsum/3g4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4t 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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [https://pdbe.org/3g4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [https://www.ebi.ac.uk/pdbsum/3g4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/UREND_METTH UREND_METTH] Involved in DNA uracil repair (PubMed:17012282, PubMed:19240141, PubMed:20129830). Recognizes DNA uracil residues within double-stranded DNA and initiates DNA-U repair by endonucleotic incision on the 5'-side of the 2'-d-uridine residue, irrespective of the nature of the opposing nucleotide (PubMed:17012282, PubMed:19240141, PubMed:20129830). In addition, acts as an apurinic/apyrimidinic (AP) endonuclease hydrolyzing the DNA phosphodiester backbone immediately at the 5'-side of AP sites, and as a 3'-5' exonuclease (PubMed:15725624, PubMed:17012282). Strongly binds to double-stranded DNA (PubMed:15725624).<ref>PMID:15725624</ref> <ref>PMID:17012282</ref> <ref>PMID:19240141</ref> <ref>PMID:20129830</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Exodeoxyribonuclease III]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metth~~]]	+	[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
-	[[Category: Dickmanns, A]]	+	[[Category: Dickmanns A]]
-	[[Category: Ficner, R]]	+	[[Category: Ficner R]]
-	[[Category: Lakomek, K]]	+	[[Category: Lakomek K]]
-	~~[[Category: Double-stranded dna]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Inorganic phosphate]]~~	+
-	~~[[Category: Mg2+]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 07:55, 9 March 2022

OCA — Wed, 09 Mar 2022 07:55:38 GMT

←Older revision		Revision as of 07:55, 9 March 2022
Line 1:		Line 1:

	==Mth0212 (WT) in complex with a 7bp dsDNA==		==Mth0212 (WT) in complex with a 7bp dsDNA==
-	<StructureSection load='3g4t' size='340' side='right' caption='[[3g4t]], [[Resolution\|resolution]] 2.64Å' scene=''>	+	<StructureSection load='3g4t' size='340' side='right'caption='[[3g4t]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g4t]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G4T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g4t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UPS:2-DEOXY-5-O-THIOPHOSPHONOURIDINE'>UPS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UPS:2-DEOXY-5-O-THIOPHOSPHONOURIDINE'>UPS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0a\|3g0a]], [[3g0r\|3g0r]], [[3g1k\|3g1k]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g3y\|3g3y]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0a\|3g0a]], [[3g0r\|3g0r]], [[3g1k\|3g1k]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g3y\|3g3y]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [~~http~~://pdbe.org/3g4t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g4t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4t 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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [https://pdbe.org/3g4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [https://www.ebi.ac.uk/pdbsum/3g4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4t ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4t_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4t_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 3g4t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3g4t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Exodeoxyribonuclease III]]		[[Category: Exodeoxyribonuclease III]]
		+	[[Category: Large Structures]]
	[[Category: Metth]]		[[Category: Metth]]
	[[Category: Dickmanns, A]]		[[Category: Dickmanns, A]]

OCA at 06:56, 1 November 2017

OCA — Wed, 01 Nov 2017 06:56:55 GMT

←Older revision		Revision as of 06:56, 1 November 2017
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		+
	==Mth0212 (WT) in complex with a 7bp dsDNA==		==Mth0212 (WT) in complex with a 7bp dsDNA==
	<StructureSection load='3g4t' size='340' side='right' caption='[[3g4t]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='3g4t' size='340' side='right' caption='[[3g4t]], [[Resolution\|resolution]] 2.64Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [http://pdbe.org/3g4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [http://www.ebi.ac.uk/pdbsum/3g4t 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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [http://pdbe.org/3g4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [http://www.ebi.ac.uk/pdbsum/3g4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4t ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 3g4t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3g4t" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Exonuclease\|Exonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:59, 10 February 2016

OCA — Wed, 10 Feb 2016 04:59:32 GMT

←Older revision		Revision as of 04:59, 10 February 2016
Line 8:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [http://www.ebi.ac.uk/pdbsum/3g4t 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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [http://pdbe.org/3g4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [http://www.ebi.ac.uk/pdbsum/3g4t PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g4t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3g4t" style="background-color:#fffaf0;"></div>

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

OCA at 23:05, 3 January 2015

OCA — Sat, 03 Jan 2015 23:05:22 GMT

←Older revision		Revision as of 23:05, 3 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3g4t\| PDB=3g4t \| SCENE= }}~~	+	==Mth0212 (WT) in complex with a 7bp dsDNA==
-	===Mth0212 (WT) in complex with a 7bp dsDNA===	+	<StructureSection load='3g4t' size='340' side='right' caption='[[3g4t]], [[Resolution\|resolution]] 2.64Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20434457}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g4t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UPS:2-DEOXY-5-O-THIOPHOSPHONOURIDINE'>UPS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0a\|3g0a]], [[3g0r\|3g0r]], [[3g1k\|3g1k]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g3y\|3g3y]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </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=3g4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4t RCSB], [http://www.ebi.ac.uk/pdbsum/3g4t PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4t_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus DeltaH, an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus DeltaH exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic/apurinic site endonuclease and 3'-->5'exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single-step reaction thus substituting the two-step pathway that requires the consecutive action of UDG and apyrimidinic/apurinic site endonuclease. In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A, suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153, and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occurring thymidine and cytosine residues in double-stranded DNA.

-	~~==About this Structure==~~	+	Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA.,Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R J Mol Biol. 2010 Jun 18;399(4):604-17. Epub 2010 Apr 29. PMID:20434457<ref>PMID:20434457</ref>
-	~~[[3g4t]] is a~~ 4 ~~chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Metth Metth]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3G4T OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Exonuclease\|Exonuclease]]		*[[Exonuclease\|Exonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020434457</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Exodeoxyribonuclease III]]		[[Category: Exodeoxyribonuclease III]]
	[[Category: Metth]]		[[Category: Metth]]
-	[[Category: Dickmanns, A.]]	+	[[Category: Dickmanns, A]]
-	[[Category: Ficner, R.]]	+	[[Category: Ficner, R]]
-	[[Category: Lakomek, K.]]	+	[[Category: Lakomek, K]]
	[[Category: Double-stranded dna]]		[[Category: Double-stranded dna]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]

OCA at 03:24, 13 February 2014

OCA — Thu, 13 Feb 2014 03:24:54 GMT

←Older revision		Revision as of 03:24, 13 February 2014
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-	[[Image:3g4t.png\|left\|200px]]
-
	{{STRUCTURE_3g4t\| PDB=3g4t \| SCENE= }}		{{STRUCTURE_3g4t\| PDB=3g4t \| SCENE= }}
-
	===Mth0212 (WT) in complex with a 7bp dsDNA===		===Mth0212 (WT) in complex with a 7bp dsDNA===
-
	{{ABSTRACT_PUBMED_20434457}}		{{ABSTRACT_PUBMED_20434457}}

	==About this Structure==		==About this Structure==
-	[[3g4t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].	+	[[3g4t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].

	==See Also==		==See Also==
Line 14:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:020434457</ref><~~ref~~ group="xtra"~~>PMID:017012282<~~/~~ref><ref group="xtra">PMID:020417641</ref~~><references ~~group="xtra"~~/>	+	<ref group="xtra">PMID:020434457</ref><references group="xtra"/><references/>
	[[Category: Exodeoxyribonuclease III]]		[[Category: Exodeoxyribonuclease III]]
-	[[Category: ~~Methanothermobacter thermautotrophicus~~]]	+	[[Category: Metth]]
	[[Category: Dickmanns, A.]]		[[Category: Dickmanns, A.]]
	[[Category: Ficner, R.]]		[[Category: Ficner, R.]]

OCA at 16:24, 20 October 2012

OCA — Sat, 20 Oct 2012 16:24:47 GMT

←Older revision		Revision as of 16:24, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3g4t]] is a 4 chain structure ~~of [[Exonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].	+	[[3g4t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].

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

OCA at 21:36, 26 July 2012

OCA — Thu, 26 Jul 2012 21:36:48 GMT

←Older revision		Revision as of 21:36, 26 July 2012
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	[[Image:3g4t.png\|left\|200px]]		[[Image:3g4t.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3g4t", 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_3g4t\| PDB=3g4t \| SCENE= }}		{{STRUCTURE_3g4t\| PDB=3g4t \| SCENE= }}

	===Mth0212 (WT) in complex with a 7bp dsDNA===		===Mth0212 (WT) in complex with a 7bp dsDNA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20434457}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20434457 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20434457}}		{{ABSTRACT_PUBMED_20434457}}

	==About this Structure==		==About this Structure==
-	[[3g4t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].	+	[[3g4t]] is a 4 chain structure of [[Exonuclease]] with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].
		+
		+	==See Also==
		+	*[[Exonuclease\|Exonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20434457~~</ref><ref group="xtra">PMID:~~17012282~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020434457</ref><ref group="xtra">PMID:017012282</ref><ref group="xtra">PMID:020417641</ref><references group="xtra"/>
	[[Category: Exodeoxyribonuclease III]]		[[Category: Exodeoxyribonuclease III]]
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]

OCA: Protected "3g4t" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 20:30:44 GMT

Protected "3g4t" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:30, 14 March 2011

OCA at 20:30, 14 March 2011

OCA — Mon, 14 Mar 2011 20:30:43 GMT

←Older revision		Revision as of 20:30, 14 March 2011
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-	{{Seed}}
	[[Image:3g4t.png\|left\|200px]]		[[Image:3g4t.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~3G4T~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].	+	[[3g4t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4T OCA].

	==Reference==		==Reference==
Line 34:		Line 33:
	[[Category: Mg2+]]		[[Category: Mg2+]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 20 09:01:16 2010''