3g0a - Revision history

OCA at 15:34, 1 November 2023

OCA — Wed, 01 Nov 2023 15:34:40 GMT

←Older revision		Revision as of 15:34, 1 November 2023
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	<StructureSection load='3g0a' size='340' side='right'caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3g0a' size='340' side='right'caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G0A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G0A FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.6Å</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]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [https://pdbe.org/3g0a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [https://www.ebi.ac.uk/pdbsum/3g0a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g0a 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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [https://pdbe.org/3g0a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [https://www.ebi.ac.uk/pdbsum/3g0a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g0a 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: 2'-deoxyuridine endonuclease]]~~	+
-	~~[[Category: Ap endonuclease]]~~	+
-	~~[[Category: Coordination of two manganese ion]]~~	+
-	~~[[Category: Double-strand specific 3'-5' exonuclease]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:52, 9 March 2022

OCA — Wed, 09 Mar 2022 07:52:37 GMT

←Older revision		Revision as of 07:52, 9 March 2022
Line 1:		Line 1:

	==Mth0212 with two bound manganese ions==		==Mth0212 with two bound manganese ions==
-	<StructureSection load='3g0a' size='340' side='right' caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='3g0a' size='340' side='right'caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G0A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G0A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[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]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [~~http~~://pdbe.org/3g0a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g0a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g0a 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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [https://pdbe.org/3g0a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [https://www.ebi.ac.uk/pdbsum/3g0a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g0a 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/g0/3g0a_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g0/3g0a_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>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3g0a" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3g0a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Exodeoxyribonuclease III]]		[[Category: Exodeoxyribonuclease III]]
		+	[[Category: Large Structures]]
	[[Category: Metth]]		[[Category: Metth]]
	[[Category: Dickmanns, A]]		[[Category: Dickmanns, A]]

OCA at 06:53, 1 November 2017

OCA — Wed, 01 Nov 2017 06:53:39 GMT

←Older revision		Revision as of 06:53, 1 November 2017
Line 1:		Line 1:
		+
	==Mth0212 with two bound manganese ions==		==Mth0212 with two bound manganese ions==
	<StructureSection load='3g0a' size='340' side='right' caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3g0a' size='340' side='right' caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' 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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [http://pdbe.org/3g0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [http://www.ebi.ac.uk/pdbsum/3g0a 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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [http://pdbe.org/3g0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [http://www.ebi.ac.uk/pdbsum/3g0a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g0a ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 3g0a" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3g0a" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Exonuclease\|Exonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:49, 7 February 2016

OCA — Sun, 07 Feb 2016 02:49:37 GMT

←Older revision		Revision as of 02:49, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3g0a' size='340' side='right' caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3g0a' size='340' side='right' caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G0A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G0A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[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=~~145262 Methanothermobacter thermautotrophicus~~])</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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [http://www.ebi.ac.uk/pdbsum/3g0a 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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [http://pdbe.org/3g0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [http://www.ebi.ac.uk/pdbsum/3g0a PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 17:
	<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=3g0a 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 3g0a" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[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 08:14, 20 January 2015

OCA — Tue, 20 Jan 2015 08:14:32 GMT

←Older revision		Revision as of 08:14, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G0A FirstGlance]. <br>		<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G0A FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]</td></tr>
-	<tr><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=145262 Methanothermobacter thermautotrophicus])</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=145262 Methanothermobacter thermautotrophicus])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [http://www.ebi.ac.uk/pdbsum/3g0a 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=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [http://www.ebi.ac.uk/pdbsum/3g0a PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Exodeoxyribonuclease III]]		[[Category: Exodeoxyribonuclease III]]
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Dickmanns, A.]]	+	[[Category: Dickmanns, A]]
-	[[Category: Ficner, R.]]	+	[[Category: Ficner, R]]
-	[[Category: Lakomek, K.]]	+	[[Category: Lakomek, K]]
	[[Category: 2'-deoxyuridine endonuclease]]		[[Category: 2'-deoxyuridine endonuclease]]
	[[Category: Ap endonuclease]]		[[Category: Ap endonuclease]]

OCA at 11:06, 29 September 2014

OCA — Mon, 29 Sep 2014 11:06:55 GMT

←Older revision		Revision as of 11:06, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3g0a.~~png~~\|~~left~~\|200px]]	+	==Mth0212 with two bound manganese ions==
		+	<StructureSection load='3g0a' size='340' side='right' caption='[[3g0a]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g0a]] is a 1 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=3G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G0A FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fzi\|3fzi]], [[3g00\|3g00]], [[3g0r\|3g0r]], [[3g2c\|3g2c]], [[3g2d\|3g2d]], [[3g38\|3g38]], [[3g3c\|3g3c]], [[3g1k\|3g1k]], [[3g3y\|3g3y]], [[3g4t\|3g4t]], [[3g8v\|3g8v]], [[3g91\|3g91]], [[3ga6\|3ga6]]</td></tr>
		+	<tr><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=145262 Methanothermobacter thermautotrophicus])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g0a RCSB], [http://www.ebi.ac.uk/pdbsum/3g0a 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/g0/3g0a_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.

-	~~{{STRUCTURE_3g0a\| PDB=3g0a \| SCENE= }}~~	+	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>

-	~~===Mth0212 with two bound manganese ions===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20434457}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3g0a]] is~~ a ~~1 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=3G0A OCA].~~	+

	==See Also==		==See Also==
	*[[Exonuclease\|Exonuclease]]		*[[Exonuclease\|Exonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020434457<~~/~~ref~~><~~ref group="xtra">PMID:017012282</ref><ref group="xtra">PMID:020417641</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Exodeoxyribonuclease III]]		[[Category: Exodeoxyribonuclease III]]
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]

OCA at 05:23, 20 October 2012

OCA — Sat, 20 Oct 2012 05:23:12 GMT

←Older revision		Revision as of 05:23, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3g0a]] is a 1 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=3G0A OCA].	+	[[3g0a]] is a 1 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=3G0A OCA].

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

OCA at 09:52, 25 July 2012

OCA — Wed, 25 Jul 2012 09:52:57 GMT

←Older revision		Revision as of 09:52, 25 July 2012
Line 1:		Line 1:
	[[Image:3g0a.png\|left\|200px]]		[[Image:3g0a.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3g0a", 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_3g0a\| PDB=3g0a \| SCENE= }}		{{STRUCTURE_3g0a\| PDB=3g0a \| SCENE= }}

	===Mth0212 with two bound manganese ions===		===Mth0212 with two bound manganese ions===

-
-	<!--
-	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==
-	[[3g0a]] is a 1 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=3G0A OCA].	+	[[3g0a]] is a 1 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=3G0A 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 "3g0a" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 18:42:47 GMT

Protected "3g0a" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:42, 14 March 2011

OCA at 18:42, 14 March 2011

OCA — Mon, 14 Mar 2011 18:42:43 GMT

←Older revision		Revision as of 18:42, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3g0a.png\|left\|200px]]		[[Image:3g0a.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~3G0A~~ is a 1 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=3G0A OCA].	+	[[3g0a]] is a 1 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=3G0A OCA].

	==Reference==		==Reference==
Line 34:		Line 33:
	[[Category: Double-strand specific 3'-5' exonuclease]]		[[Category: Double-strand specific 3'-5' exonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 20 08:57:54 2010''