4c8n - Revision history

OCA at 11:09, 9 May 2024

2024-05-09T11:09:43Z

←Older revision		Revision as of 11:09, 9 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4c8n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[4c8n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C8N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.88Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8n OCA], [https://pdbe.org/4c8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c8n RCSB], [https://www.ebi.ac.uk/pdbsum/4c8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c8n 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=4c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8n OCA], [https://pdbe.org/4c8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c8n RCSB], [https://www.ebi.ac.uk/pdbsum/4c8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c8n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]]	+	[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.
		+
		+	Structural Insights into DNA Replication without Hydrogen Bonds.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A J Am Chem Soc. 2013 Nov 27. PMID:24283923<ref>PMID:24283923</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4c8n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:32, 7 September 2022

2022-09-07T17:32:19Z

←Older revision		Revision as of 17:32, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='4c8n' size='340' side='right'caption='[[4c8n]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='4c8n' size='340' side='right'caption='[[4c8n]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4c8n]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4C8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4c8n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C8N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</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=4c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8n OCA], [https://pdbe.org/4c8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c8n RCSB], [https://www.ebi.ac.uk/pdbsum/4c8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c8n ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4c8j\|4c8j]]~~, ~~[[4c8k\|4c8k]], [[4c8l\|4c8l]], [[4c8m\|4c8m]], [[4c8o\|4c8o]]~~<~~/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=4c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8n OCA], [~~http~~://pdbe.org/4c8n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4c8n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4c8n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4c8n ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]]
-	The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.	+
-		+
-	~~Structural Insights into DNA Replication without Hydrogen Bonds.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A J Am Chem Soc. 2013 Nov 27. PMID:24283923<ref>PMID~~:~~24283923<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 4c8n" style="background-color:#fffaf0;"><~~/~~div>~~	+
-		+
-	~~==See Also==~~	+
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25104]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Betz, K~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Diederichs, K~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: ~~Lavergne, T~~]]	+	[[Category: Betz K]]
-	[[Category: ~~Malyshev, D A~~]]	+	[[Category: Diederichs K]]
-	[[Category: ~~Marx, A~~]]	+	[[Category: Lavergne T]]
-	[[Category: ~~Romesberg, F E~~]]	+	[[Category: Malyshev DA]]
-	[[Category: ~~Welte, W~~]]	+	[[Category: Marx A]]
-	[[Category: ~~Artificial base pair~~]]	+	[[Category: Romesberg FE]]
-	[[Category: ~~Binary complex]]~~	+	[[Category: Welte W]]
-	~~[[Category: Transferase-dna complex]]~~	+
-	~~[[Category: Unnatural base pair~~]]	+

OCA at 16:34, 28 August 2019

2019-08-28T16:34:32Z

←Older revision		Revision as of 16:34, 28 August 2019
Line 1:		Line 1:

	==Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)==		==Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)==
-	<StructureSection load='4c8n' size='340' side='right' caption='[[4c8n]], [[Resolution\|resolution]] 1.88Å' scene=''>	+	<StructureSection load='4c8n' size='340' side='right'caption='[[4c8n]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4c8n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[4c8n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C8N FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4c8n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4c8n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Atcc 25104]]		[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Betz, K]]		[[Category: Betz, K]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]

OCA at 22:20, 15 November 2017

2017-11-15T22:20:37Z

←Older revision		Revision as of 22:20, 15 November 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4c8n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4c8n" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:03, 11 August 2016

2016-08-11T11:03:47Z

←Older revision		Revision as of 11:03, 11 August 2016
Line 1:		Line 1:
		+
	==Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)==		==Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)==
	<StructureSection load='4c8n' size='340' side='right' caption='[[4c8n]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='4c8n' size='340' side='right' caption='[[4c8n]], [[Resolution\|resolution]] 1.88Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c8j\|4c8j]], [[4c8k\|4c8k]], [[4c8l\|4c8l]], [[4c8m\|4c8m]], [[4c8o\|4c8o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c8j\|4c8j]], [[4c8k\|4c8k]], [[4c8l\|4c8l]], [[4c8m\|4c8m]], [[4c8o\|4c8o]]</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=4c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4c8n RCSB], [http://www.ebi.ac.uk/pdbsum/4c8n 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=4c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8n OCA], [http://pdbe.org/4c8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4c8n RCSB], [http://www.ebi.ac.uk/pdbsum/4c8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4c8n ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4c8n" style="background-color:#fffaf0;"></div>

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

OCA at 12:50, 4 January 2015

2015-01-04T12:50:46Z

←Older revision		Revision as of 12:50, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4c8n\| PDB=4c8n \| SCENE= }}~~	+	==Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)==
-	===Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)===	+	<StructureSection load='4c8n' size='340' side='right' caption='[[4c8n]], [[Resolution\|resolution]] 1.88Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24283923}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4c8n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C8N FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c8j\|4c8j]], [[4c8k\|4c8k]], [[4c8l\|4c8l]], [[4c8m\|4c8m]], [[4c8o\|4c8o]]</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=4c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4c8n RCSB], [http://www.ebi.ac.uk/pdbsum/4c8n PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.

-	~~==About this Structure==~~	+	Structural Insights into DNA Replication without Hydrogen Bonds.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A J Am Chem Soc. 2013 Nov 27. PMID:24283923<ref>PMID:24283923</ref>
-	~~[[4c8n]] is a 3 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4C8N OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:024283923</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Betz, K.]]	+	[[Category: Betz, K]]
-	[[Category: Diederichs, K.]]	+	[[Category: Diederichs, K]]
-	[[Category: Lavergne, T.]]	+	[[Category: Lavergne, T]]
-	[[Category: Malyshev, D A.]]	+	[[Category: Malyshev, D A]]
-	[[Category: Marx, A.]]	+	[[Category: Marx, A]]
-	[[Category: Romesberg, F E.]]	+	[[Category: Romesberg, F E]]
-	[[Category: Welte, W.]]	+	[[Category: Welte, W]]
	[[Category: Artificial base pair]]		[[Category: Artificial base pair]]
	[[Category: Binary complex]]		[[Category: Binary complex]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]
	[[Category: Unnatural base pair]]		[[Category: Unnatural base pair]]

OCA at 13:39, 11 December 2013

2013-12-11T13:39:45Z

←Older revision		Revision as of 13:39, 11 December 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4c8n\| PDB=4c8n \| SCENE= }}
		+	===Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)===
		+	{{ABSTRACT_PUBMED_24283923}}

-	~~The entry~~ 4c8n is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4c8n]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8N OCA].

-	~~Authors~~: Betz, K., ~~Malyshev, D~~.~~A.,~~ Lavergne, T., ~~Welte, W~~., ~~Diederichs, K~~., Romesberg, F.E., ~~Marx, A~~.	+	==Reference==
-		+	<ref group="xtra">PMID:024283923</ref><references group="xtra"/><references/>
-	~~Description~~: Binary complex ~~of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial~~ base pair ~~dNaM-d5SICS at the postinsertion site (sequence context 3)~~	+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Betz, K.]]
		+	[[Category: Diederichs, K.]]
		+	[[Category: Lavergne, T.]]
		+	[[Category: Malyshev, D A.]]
		+	[[Category: Marx, A.]]
		+	[[Category: Romesberg, F E.]]
		+	[[Category: Welte, W.]]
		+	[[Category: Artificial base pair]]
		+	[[Category: Binary complex]]
		+	[[Category: Transferase-dna complex]]
		+	[[Category: Unnatural base pair]]

OCA at 05:38, 23 October 2013

2013-10-23T05:38:06Z

←Older revision		Revision as of 05:38, 23 October 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4c8n is ON HOLD	+	The entry 4c8n is ON HOLD until Paper Publication

	Authors: Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Romesberg, F.E., Marx, A.		Authors: Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Romesberg, F.E., Marx, A.

	Description: Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)		Description: Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)

OCA: Protected "4c8n" [edit=sysop:move=sysop]

2013-10-10T05:28:11Z

Protected "4c8n" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:28, 10 October 2013

OCA: New page: '''Unreleased structure''' The entry 4c8n is ON HOLD Authors: Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Romesberg, F.E., Marx, A. Description: Binary complex o...

2013-10-10T05:28:10Z

New page: '''Unreleased structure''' The entry 4c8n is ON HOLD Authors: Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Romesberg, F.E., Marx, A. Description: Binary complex o...

New page

'''Unreleased structure'''

The entry 4c8n is ON HOLD

Authors: Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Romesberg, F.E., Marx, A.

Description: Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)