5vu7 - Revision history

OCA at 08:44, 30 September 2020

OCA — Wed, 30 Sep 2020 08:44:46 GMT

←Older revision		Revision as of 08:44, 30 September 2020
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	==TNA polymerase, open ternary complex==		==TNA polymerase, open ternary complex==
-	<StructureSection load='5vu7' size='340' side='right' caption='[[5vu7]], [[Resolution\|resolution]] 2.72Å' scene=''>	+	<StructureSection load='5vu7' size='340' side='right'caption='[[5vu7]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vu7]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VU7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vu7]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VU7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=9O4:'>9O4</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O4:'>9O4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu6\|5vu6]], [[5vu8\|5vu8]], [[5vu9\|5vu9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu6\|5vu6]], [[5vu8\|5vu8]], [[5vu9\|5vu9]]</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=5vu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu7 OCA], [http://pdbe.org/5vu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu7 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5vu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu7 OCA], [http://pdbe.org/5vu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu7 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5vu7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vu7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Thermococcus kodakaraensis atomi et al. 2004]]		[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Chaput, J C]]		[[Category: Chaput, J C]]
	[[Category: Chim, N]]		[[Category: Chim, N]]
	[[Category: Protein-nucleic acid complex]]		[[Category: Protein-nucleic acid complex]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 07:33, 13 December 2017

OCA — Wed, 13 Dec 2017 07:33:22 GMT

←Older revision		Revision as of 07:33, 13 December 2017
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	<StructureSection load='5vu7' size='340' side='right' caption='[[5vu7]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='5vu7' size='340' side='right' caption='[[5vu7]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vu7]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vu7]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=9O4:'>9O4</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O4:'>9O4</scene></td></tr>
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	<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=5vu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu7 OCA], [http://pdbe.org/5vu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu7 ProSAT]</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=5vu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu7 OCA], [http://pdbe.org/5vu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Darwinian evolution experiments carried out on xeno-nucleic acid (XNA) polymers require engineered polymerases that can faithfully and efficiently copy genetic information back and forth between DNA and XNA. However, current XNA polymerases function with inferior activity relative to their natural counterparts. Here, we report five X-ray crystal structures that illustrate the pathway by which alpha-(L)-threofuranosyl nucleic acid (TNA) triphosphates are selected and extended in a template-dependent manner using a laboratory-evolved polymerase known as Kod-RI. Structural comparison of the apo, binary, open and closed ternary, and translocated product detail an ensemble of interactions and conformational changes required to promote TNA synthesis. Close inspection of the active site in the closed ternary structure reveals a sub-optimal binding geometry that explains the slow rate of catalysis. This key piece of information, which is missing for all naturally occurring archaeal DNA polymerases, provides a framework for engineering new TNA polymerase variants.
		+
		+	Structural basis for TNA synthesis by an engineered TNA polymerase.,Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC Nat Commun. 2017 Nov 27;8(1):1810. doi: 10.1038/s41467-017-02014-0. PMID:29180809<ref>PMID:29180809</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vu7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Chaput, J C]]		[[Category: Chaput, J C]]

OCA at 07:16, 6 December 2017

OCA — Wed, 06 Dec 2017 07:16:40 GMT

←Older revision		Revision as of 07:16, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vu7 is ~~ON HOLD until Paper Publication~~	+	==TNA polymerase, open ternary complex==
-		+	<StructureSection load='5vu7' size='340' side='right' caption='[[5vu7]], [[Resolution\|resolution]] 2.72Å' scene=''>
-	~~Authors~~: ~~Chim~~, N., ~~Chaput~~, J.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vu7]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU7 FirstGlance]. <br>
-	~~Description~~: ~~TNA~~ polymerase~~, open ternary complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O4:'>9O4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu6\|5vu6]], [[5vu8\|5vu8]], [[5vu9\|5vu9]]</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=5vu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu7 OCA], [http://pdbe.org/5vu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu7 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Chaput, J C]]
	[[Category: Chim, N]]		[[Category: Chim, N]]
-	[[Category: ~~Chaput, J.C~~]]	+	[[Category: Protein-nucleic acid complex]]
		+	[[Category: Transferase-dna complex]]

OCA at 14:13, 27 September 2017

OCA — Wed, 27 Sep 2017 14:13:43 GMT

←Older revision		Revision as of 14:13, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vu7 is ON HOLD	+	The entry 5vu7 is ON HOLD until Paper Publication

	Authors: Chim, N., Chaput, J.C.		Authors: Chim, N., Chaput, J.C.
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	Description: TNA polymerase, open ternary complex		Description: TNA polymerase, open ternary complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chaput, J.C]]
	[[Category: Chim, N]]		[[Category: Chim, N]]
		+	[[Category: Chaput, J.C]]

OCA: Protected "5vu7" [edit=sysop:move=sysop]

OCA — Wed, 24 May 2017 11:50:53 GMT

Protected "5vu7" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:50, 24 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vu7 is ON HOLD Authors: Chim, N., Chaput, J.C. Description: TNA polymerase, open ternary complex Category: Unreleased Structures [[Category: C...

OCA — Wed, 24 May 2017 11:50:52 GMT

New page: '''Unreleased structure''' The entry 5vu7 is ON HOLD Authors: Chim, N., Chaput, J.C. Description: TNA polymerase, open ternary complex Category: Unreleased Structures [[Category: C...

New page

'''Unreleased structure'''

The entry 5vu7 is ON HOLD

Authors: Chim, N., Chaput, J.C.

Description: TNA polymerase, open ternary complex
[[Category: Unreleased Structures]]
[[Category: Chaput, J.C]]
[[Category: Chim, N]]