3px0 - Revision history

OCA at 13:34, 1 March 2024

OCA — Fri, 01 Mar 2024 13:34:28 GMT

←Older revision		Revision as of 13:34, 1 March 2024
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	<StructureSection load='3px0' size='340' side='right'caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3px0' size='340' side='right'caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_kaustophilus"_prickett_1928 "bacillus~~ kaustophilus~~" prickett 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DCP:2~~-~~DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.73Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~DOC~~:2,3-~~DIDEOXYCYTIDINE~~-5-~~MONOPHOSPHATE~~'>~~DOC~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[3pv8\|3pv8]], [[3px4\|3px4]], [[3px6\|3px6]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">polA, GK2730~~ (~~[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928]~~)~~</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=3px0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px0 OCA], [https://pdbe.org/3px0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3px0 RCSB], [https://www.ebi.ac.uk/pdbsum/3px0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3px0 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=3px0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px0 OCA], [https://pdbe.org/3px0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3px0 RCSB], [https://www.ebi.ac.uk/pdbsum/3px0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3px0 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]
-	Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C*A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. ~~These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly~~.	+

-	Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.,Wang W, Hellinga HW, Beese LS Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17644-8. Epub 2011 Oct 17. PMID:22006298<ref>PMID:22006298</ref>	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3px0" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ kaustophilus ~~prickett 1928]]~~	+	[[Category: Geobacillus kaustophilus]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beese~~, L S~~]]	+	[[Category: Beese LS]]
-	[[Category: Wang, W]]	+	[[Category: Wang W]]
-	~~[[Category: Closed conformation]]~~	+
-	~~[[Category: Cytosine-adenine]]~~	+
-	~~[[Category: Dna polymerase i]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 08:59, 25 May 2022

OCA — Wed, 25 May 2022 08:59:50 GMT

←Older revision		Revision as of 08:59, 25 May 2022
Line 3:		Line 3:
	<StructureSection load='3px0' size='340' side='right'caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3px0' size='340' side='right'caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pv8\|3pv8]], [[3px4\|3px4]], [[3px6\|3px6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pv8\|3pv8]], [[3px4\|3px4]], [[3px6\|3px6]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</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=3px0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px0 OCA], [~~http~~://pdbe.org/3px0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3px0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3px0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3px0 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=3px0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px0 OCA], [https://pdbe.org/3px0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3px0 RCSB], [https://www.ebi.ac.uk/pdbsum/3px0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3px0 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3px0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3px0" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:33, 17 July 2019

OCA — Wed, 17 Jul 2019 11:33:07 GMT

←Older revision		Revision as of 11:33, 17 July 2019
Line 1:		Line 1:

	==Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation==		==Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation==
-	<StructureSection load='3px0' size='340' side='right' caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='3px0' size='340' side='right'caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	[[Category: Bacillus kaustophilus prickett 1928]]		[[Category: Bacillus kaustophilus prickett 1928]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Wang, W]]		[[Category: Wang, W]]

OCA at 11:29, 10 December 2016

OCA — Sat, 10 Dec 2016 11:29:43 GMT

←Older revision		Revision as of 11:29, 10 December 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation==		==Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation==
	<StructureSection load='3px0' size='340' side='right' caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3px0' size='340' side='right' caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_kaustophilus Geobacillus~~ kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pv8\|3pv8]], [[3px4\|3px4]], [[3px6\|3px6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pv8\|3pv8]], [[3px4\|3px4]], [[3px6\|3px6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 ~~Geobacillus~~ kaustophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</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=3px0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3px0 RCSB], [http://www.ebi.ac.uk/pdbsum/3px0 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=3px0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px0 OCA], [http://pdbe.org/3px0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3px0 RCSB], [http://www.ebi.ac.uk/pdbsum/3px0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3px0 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	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 3px0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus kaustophilus prickett 1928]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Geobacillus kaustophilus]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Wang, W]]		[[Category: Wang, W]]

OCA at 11:21, 9 December 2014

OCA — Tue, 09 Dec 2014 11:21:23 GMT

←Older revision		Revision as of 11:21, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3px0.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation==
		+	<StructureSection load='3px0' size='340' side='right' caption='[[3px0]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PX0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pv8\|3pv8]], [[3px4\|3px4]], [[3px6\|3px6]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</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=3px0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3px0 RCSB], [http://www.ebi.ac.uk/pdbsum/3px0 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C*A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.

-	~~{{STRUCTURE_3px0\| PDB=3px0 \| SCENE= }}~~	+	Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.,Wang W, Hellinga HW, Beese LS Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17644-8. Epub 2011 Oct 17. PMID:22006298<ref>PMID:22006298</ref>

-	~~===Crystal Structure~~ of ~~Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22006298}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3px0]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:022006298<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]
-	[[Category: Beese, L S.]]	+	[[Category: Beese, L S]]
-	[[Category: Wang, W.]]	+	[[Category: Wang, W]]
	[[Category: Closed conformation]]		[[Category: Closed conformation]]
	[[Category: Cytosine-adenine]]		[[Category: Cytosine-adenine]]

OCA at 05:21, 20 October 2012

OCA — Sat, 20 Oct 2012 05:21:22 GMT

←Older revision		Revision as of 05:21, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3px0]] is a 6 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].	+	[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].

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

OCA at 09:47, 25 July 2012

OCA — Wed, 25 Jul 2012 09:47:10 GMT

←Older revision		Revision as of 09:47, 25 July 2012
Line 1:		Line 1:
	[[Image:3px0.png\|left\|200px]]		[[Image:3px0.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3px0", 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_3px0\| PDB=3px0 \| SCENE= }}		{{STRUCTURE_3px0\| PDB=3px0 \| SCENE= }}

	===Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation===		===Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22006298}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22006298 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22006298}}		{{ABSTRACT_PUBMED_22006298}}

	==About this Structure==		==About this Structure==
-	[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].	+	[[3px0]] is a 6 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==

OCA at 07:37, 2 November 2011

OCA — Wed, 02 Nov 2011 07:37:36 GMT

←Older revision		Revision as of 07:37, 2 November 2011
Line 11:		Line 11:
	===Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation===		===Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22006298}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22006298 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22006298}}

	==About this Structure==		==About this Structure==
	[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].		[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022006298</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]

OCA at 10:17, 30 October 2011

OCA — Sun, 30 Oct 2011 10:17:37 GMT

←Older revision		Revision as of 10:17, 30 October 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3px0.png\|left\|200px]]

-	The ~~entry 3px0~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3px0", 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_3px0\| PDB=3px0 \| SCENE= }}

-	~~Authors: Wang, W., Beese, L.S.~~	+	===Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation===

-	~~Description~~: DNA polymerase complex 1	+
		+	==About this Structure==
		+	[[3px0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX0 OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Geobacillus kaustophilus]]
		+	[[Category: Beese, L S.]]
		+	[[Category: Wang, W.]]
		+	[[Category: Closed conformation]]
		+	[[Category: Cytosine-adenine]]
		+	[[Category: Dna polymerase i]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Transferase-dna complex]]

OCA at 05:55, 14 September 2011

OCA — Wed, 14 Sep 2011 05:55:09 GMT

←Older revision		Revision as of 05:55, 14 September 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3px0 is ON HOLD	+	The entry 3px0 is ON HOLD until Paper Publication

	Authors: Wang, W., Beese, L.S.		Authors: Wang, W., Beese, L.S.

	Description: DNA polymerase complex 1		Description: DNA polymerase complex 1