1kea - Revision history

OCA at 07:46, 7 February 2024

2024-02-07T07:46:13Z

←Older revision		Revision as of 07:46, 7 February 2024
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	<StructureSection load='1kea' size='340' side='right'caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kea' size='340' side='right'caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [https://pdbe.org/1kea PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [https://www.ebi.ac.uk/pdbsum/1kea PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kea 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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [https://pdbe.org/1kea PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [https://www.ebi.ac.uk/pdbsum/1kea PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kea ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~GTMR_METTF GTMR_METTF~~]~~] Could act in~~ DNA ~~repair. Restriction methylase M.mthtI~~, ~~which is encoded by this plasmid, generates~~ 5-methylcytosine ~~which is, especially under thermophilic conditions, subject to deamination resulting in G~~-T mismatches. ~~This protein could correct these~~ mismatches.	+	[https://www.uniprot.org/uniprot/MIG_METTF MIG_METTF] DNA glycosylase that excises thymine from T/G mismatches and uracil from U/G mismatches (PubMed:8895589, PubMed:11788726). Acts as a repair enzyme able to counteract the mutagenic effect of spontaneous hydrolytic deamination of DNA 5-methylcytosine (5-meC) residues that leads to the formation of T/G mismatches (PubMed:8895589). May also repair U/G mismatches arising from hydrolytic deamination of DNA cytosine residues (PubMed:8895589). G/G, A/G, T/C and U/C are minor substrates (PubMed:8895589, PubMed:11788726).<ref>PMID:11788726</ref> <ref>PMID:8895589</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1kea 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=1kea ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The repair of T:G mismatches in DNA is key for maintaining bacterial restriction/modification systems and gene silencing in higher eukaryotes. T:G mismatch repair can be initiated by a specific mismatch glycosylase (MIG) that is homologous to the helix-hairpin-helix (HhH) DNA repair enzymes. Here, we present a 2.0 A resolution crystal structure and complementary mutagenesis results for this thermophilic HhH MIG enzyme. The results suggest that MIG distorts the target thymine nucleotide by twisting the thymine base approximately 90 degrees away from its normal anti position within DNA. We propose that functionally significant differences exist in DNA repair enzyme extrahelical nucleotide binding and catalysis that are characteristic of whether the target base is damaged or is a normal base within a mispair. These results explain why pure HhH DNA glycosylases and combined glycosylase/AP lyases cannot be interconverted by simply altering their functional group chemistry, and how broad-specificity DNA glycosylase enzymes may weaken the glycosylic linkage to allow a variety of damaged DNA bases to be excised.
-
-	Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases.,Mol CD, Arvai AS, Begley TJ, Cunningham RP, Tainer JA J Mol Biol. 2002 Jan 18;315(3):373-84. PMID:11786018<ref>PMID:11786018</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kea" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Arvai, A S~~]]	+	[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: ~~Begley, T J~~]]	+	[[Category: Arvai AS]]
-	[[Category: ~~Cunningham, R P~~]]	+	[[Category: Begley TJ]]
-	[[Category: ~~Mol, C D~~]]	+	[[Category: Cunningham RP]]
-	[[Category: ~~Tainer, J A~~]]	+	[[Category: Mol CD]]
-	[[Category: ~~Base twisting]]~~	+	[[Category: Tainer JA]]
-	~~[[Category: Dna glycosylase]]~~	+
-	~~[[Category: Dna mismatch]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Methylation~~]]	+

OCA at 06:52, 11 August 2021

2021-08-11T06:52:50Z

←Older revision		Revision as of 06:52, 11 August 2021
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	<StructureSection load='1kea' size='340' side='right'caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kea' size='340' side='right'caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KEA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [~~http~~://pdbe.org/1kea PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kea PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kea 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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [https://pdbe.org/1kea PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [https://www.ebi.ac.uk/pdbsum/1kea PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kea ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GTMR_METTF GTMR_METTF]] Could act in DNA repair. Restriction methylase M.mthtI, which is encoded by this plasmid, generates 5-methylcytosine which is, especially under thermophilic conditions, subject to deamination resulting in G-T mismatches. This protein could correct these mismatches.	+	[[https://www.uniprot.org/uniprot/GTMR_METTF GTMR_METTF]] Could act in DNA repair. Restriction methylase M.mthtI, which is encoded by this plasmid, generates 5-methylcytosine which is, especially under thermophilic conditions, subject to deamination resulting in G-T mismatches. This protein could correct these mismatches.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:35, 6 November 2019

2019-11-06T09:35:36Z

←Older revision		Revision as of 09:35, 6 November 2019
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	==STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE==		==STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE==
-	<StructureSection load='1kea' size='340' side='right' caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1kea' size='340' side='right'caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1kea" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kea" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arvai, A S]]		[[Category: Arvai, A S]]
	[[Category: Begley, T J]]		[[Category: Begley, T J]]

OCA at 21:42, 24 January 2018

2018-01-24T21:42:00Z

←Older revision		Revision as of 21:42, 24 January 2018
Line 1:		Line 1:
		+
	==STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE==		==STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE==
	<StructureSection load='1kea' size='340' side='right' caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kea' size='340' side='right' caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [http://pdbe.org/1kea PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [http://www.ebi.ac.uk/pdbsum/1kea 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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [http://pdbe.org/1kea PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [http://www.ebi.ac.uk/pdbsum/1kea PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kea ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/ke/1kea_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ke/1kea_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 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1kea" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kea" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:26, 7 February 2016

2016-02-07T05:26:36Z

←Older revision		Revision as of 05:26, 7 February 2016
Line 16:		Line 16:
	<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=1kea ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:17, 9 September 2015

2015-09-09T22:17:14Z

←Older revision		Revision as of 22:17, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1kea' size='340' side='right' caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kea' size='340' side='right' caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kea]] 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=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kea]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [http://www.ebi.ac.uk/pdbsum/1kea 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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [http://pdbe.org/1kea PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [http://www.ebi.ac.uk/pdbsum/1kea PDBsum]</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 1kea" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Arvai, A S]]		[[Category: Arvai, A S]]
	[[Category: Begley, T J]]		[[Category: Begley, T J]]

OCA at 08:12, 24 December 2014

2014-12-24T08:12:06Z

←Older revision		Revision as of 08:12, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kea]] 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=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kea]] 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=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [http://www.ebi.ac.uk/pdbsum/1kea 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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [http://www.ebi.ac.uk/pdbsum/1kea PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GTMR_METTF GTMR_METTF]] Could act in DNA repair. Restriction methylase M.mthtI, which is encoded by this plasmid, generates 5-methylcytosine which is, especially under thermophilic conditions, subject to deamination resulting in G-T mismatches. This protein could correct these mismatches.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Arvai, A S.]]	+	[[Category: Arvai, A S]]
-	[[Category: Begley, T J.]]	+	[[Category: Begley, T J]]
-	[[Category: Cunningham, R P.]]	+	[[Category: Cunningham, R P]]
-	[[Category: Mol, C D.]]	+	[[Category: Mol, C D]]
-	[[Category: Tainer, J A.]]	+	[[Category: Tainer, J A]]
	[[Category: Base twisting]]		[[Category: Base twisting]]
	[[Category: Dna glycosylase]]		[[Category: Dna glycosylase]]

OCA at 09:04, 3 October 2014

2014-10-03T09:04:44Z

←Older revision		Revision as of 09:04, 3 October 2014
Line 1:		Line 1:
-	[[~~Image~~:1kea.~~png\|left~~\|200px]]	+	==STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE==
		+	<StructureSection load='1kea' size='340' side='right' caption='[[1kea]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kea]] 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=1KEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<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=1kea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kea OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kea RCSB], [http://www.ebi.ac.uk/pdbsum/1kea 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/ke/1kea_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 repair of T:G mismatches in DNA is key for maintaining bacterial restriction/modification systems and gene silencing in higher eukaryotes. T:G mismatch repair can be initiated by a specific mismatch glycosylase (MIG) that is homologous to the helix-hairpin-helix (HhH) DNA repair enzymes. Here, we present a 2.0 A resolution crystal structure and complementary mutagenesis results for this thermophilic HhH MIG enzyme. The results suggest that MIG distorts the target thymine nucleotide by twisting the thymine base approximately 90 degrees away from its normal anti position within DNA. We propose that functionally significant differences exist in DNA repair enzyme extrahelical nucleotide binding and catalysis that are characteristic of whether the target base is damaged or is a normal base within a mispair. These results explain why pure HhH DNA glycosylases and combined glycosylase/AP lyases cannot be interconverted by simply altering their functional group chemistry, and how broad-specificity DNA glycosylase enzymes may weaken the glycosylic linkage to allow a variety of damaged DNA bases to be excised.

-	~~{{STRUCTURE_1kea\| PDB=1kea \| SCENE= }}~~	+	Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases.,Mol CD, Arvai AS, Begley TJ, Cunningham RP, Tainer JA J Mol Biol. 2002 Jan 18;315(3):373-84. PMID:11786018<ref>PMID:11786018</ref>

-	~~===STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11786018}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kea]] 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=1KEA OCA].~~	+

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011786018<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Arvai, A S.]]		[[Category: Arvai, A S.]]

OCA at 05:42, 20 October 2012

2012-10-20T05:42:35Z

←Older revision		Revision as of 05:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kea]] is a 1 chain structure ~~of [[DNA glycosylate]]~~ 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=1KEA OCA].	+	[[1kea]] 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=1KEA OCA].

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

OCA: Protected "1kea" [edit=sysop:move=sysop]

2012-07-25T10:53:45Z

Protected "1kea" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:53, 25 July 2012