1njz - Revision history

OCA at 09:21, 16 August 2023

2023-08-16T09:21:08Z

←Older revision		Revision as of 09:21, 16 August 2023
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	<StructureSection load='1njz' size='340' side='right'caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1njz' size='340' side='right'caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GLC:ALPHA~~-~~D-GLUCOSE'>GLC</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~activity~~'><~~td class="sblockLbl"~~><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [https://pdbe.org/1njz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [https://www.ebi.ac.uk/pdbsum/1njz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njz 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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [https://pdbe.org/1njz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [https://www.ebi.ac.uk/pdbsum/1njz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.	+	[https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980]]~~	+	[[Category: Geobacillus stearothermophilus]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beese~~, L S~~]]	+	[[Category: Beese LS]]
-	[[Category: Johnson~~, S J]]~~	+	[[Category: Johnson SJ]]
-	~~[[Category: Dna mismatch]]~~	+
-	~~[[Category: Dna polymerase i]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Klenow fragment]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 07:03, 25 August 2021

2021-08-25T07:03:44Z

←Older revision		Revision as of 07:03, 25 August 2021
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	<StructureSection load='1njz' size='340' side='right'caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1njz' size='340' side='right'caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJZ 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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=~~SUC~~:~~SUCROSE~~'>~~SUC~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [~~http~~://pdbe.org/1njz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1njz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1njz 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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [https://pdbe.org/1njz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [https://www.ebi.ac.uk/pdbsum/1njz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.	+	[[https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:25, 20 November 2019

2019-11-20T18:25:38Z

←Older revision		Revision as of 18:25, 20 November 2019
Line 1:		Line 1:

	==CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE==		==CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE==
-	<StructureSection load='1njz' size='340' side='right' caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1njz' size='340' side='right'caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Johnson, S J]]		[[Category: Johnson, S J]]

OCA at 07:13, 7 February 2018

2018-02-07T07:13:19Z

←Older revision		Revision as of 07:13, 7 February 2018
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		+
	==CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE==		==CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE==
	<StructureSection load='1njz' size='340' side='right' caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1njz' size='340' side='right' caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [http://pdbe.org/1njz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [http://www.ebi.ac.uk/pdbsum/1njz 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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [http://pdbe.org/1njz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [http://www.ebi.ac.uk/pdbsum/1njz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1njz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1njz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1njz_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 30:
	</div>		</div>
	<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1njz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:51, 7 February 2016

2016-02-07T12:51:22Z

←Older revision		Revision as of 12:51, 7 February 2016
Line 18:		Line 18:
	<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=1njz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:39, 10 September 2015

2015-09-10T01:39:44Z

←Older revision		Revision as of 01:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1njz' size='340' side='right' caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1njz' size='340' side='right' caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJZ 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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>		</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [http://www.ebi.ac.uk/pdbsum/1njz 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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [http://pdbe.org/1njz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [http://www.ebi.ac.uk/pdbsum/1njz PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~DPO1_BACST DPO1_BACST~~]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.	+	[[http://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	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 1njz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Geobacillus stearothermophilus]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Johnson, S J]]		[[Category: Johnson, S J]]

OCA at 15:14, 24 December 2014

2014-12-24T15:14:28Z

←Older revision		Revision as of 15:14, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [http://www.ebi.ac.uk/pdbsum/1njz 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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [http://www.ebi.ac.uk/pdbsum/1njz PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO1_BACST DPO1_BACST]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Beese, L S.]]	+	[[Category: Beese, L S]]
-	[[Category: Johnson, S J.]]	+	[[Category: Johnson, S J]]
	[[Category: Dna mismatch]]		[[Category: Dna mismatch]]
	[[Category: Dna polymerase i]]		[[Category: Dna polymerase i]]

OCA at 16:01, 28 September 2014

2014-09-28T16:01:44Z

←Older revision		Revision as of 16:01, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1njz.~~png~~\|~~left~~\|200px]]	+	==CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE==
		+	<StructureSection load='1njz' size='340' side='right' caption='[[1njz]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1njw\|1njw]], [[1njx\|1njx]], [[1njy\|1njy]], [[1nk0\|1nk0]], [[1nk4\|1nk4]], [[1nk5\|1nk5]], [[1nk6\|1nk6]], [[1nk7\|1nk7]], [[1nk8\|1nk8]], [[1nk9\|1nk9]], [[1nkb\|1nkb]], [[1nkc\|1nkc]], [[1nke\|1nke]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1njz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njz RCSB], [http://www.ebi.ac.uk/pdbsum/1njz 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/nj/1njz_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 ==
		+	Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.

-	~~{{STRUCTURE_1njz\| PDB=1njz \| SCENE= }}~~	+	Structures of mismatch replication errors observed in a DNA polymerase.,Johnson SJ, Beese LS Cell. 2004 Mar 19;116(6):803-16. PMID:15035983<ref>PMID:15035983</ref>

-	~~===CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15035983}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1njz]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015035983<~~/~~ref~~><~~ref group="xtra">PMID:012649320</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]

OCA at 06:42, 20 October 2012

2012-10-20T06:42:24Z

←Older revision		Revision as of 06:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1njz]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA].	+	[[1njz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJZ OCA].

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

OCA at 14:03, 25 July 2012

2012-07-25T14:03:06Z

←Older revision		Revision as of 14:03, 25 July 2012
Line 1:		Line 1:
	[[Image:1njz.png\|left\|200px]]		[[Image:1njz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1njz", 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_1njz\| PDB=1njz \| SCENE= }}		{{STRUCTURE_1njz\| PDB=1njz \| SCENE= }}

	===CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE===		===CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15035983}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15035983 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15035983}}		{{ABSTRACT_PUBMED_15035983}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[DNA polymerase]]	+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15035983~~</ref><ref group="xtra">PMID:~~12649320~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015035983</ref><ref group="xtra">PMID:012649320</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
Line 35:		Line 24:
	[[Category: Klenow fragment]]		[[Category: Klenow fragment]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
-	[[Category: Transferase/dna complex]]	+	[[Category: Transferase-dna complex]]