5vu6 - Revision history

OCA at 13:58, 4 October 2023

OCA — Wed, 04 Oct 2023 13:58:39 GMT

←Older revision		Revision as of 13:58, 4 October 2023
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	<StructureSection load='5vu6' size='340' side='right'caption='[[5vu6]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5vu6' size='340' side='right'caption='[[5vu6]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vu6]] 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=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5VU6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vu6]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis] 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=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VU6 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN~~-3~~-YL+DIHYDROGEN+PHOSPHATE'>FA2</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]] 3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5vu5\|5vu5]], [[5vu7\|5vu7]], [[5vu8\|5vu8]], [[5vu9\|5vu9]]</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></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'>[https://proteopedia.org/fgij/fg.htm?mol=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [https://pdbe.org/5vu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [https://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 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=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [~~http~~://pdbe.org/5vu6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D0VWU9_THEKO D0VWU9_THEKO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chaput, J C~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Chim, N~~]]	+	[[Category: Thermococcus kodakarensis]]
-	[[Category: ~~Protein-nucleic acid complex~~]]	+	[[Category: Chaput JC]]
-	[[Category: ~~Transferase-dna complex~~]]	+	[[Category: Chim N]]

OCA at 08:44, 30 September 2020

OCA — Wed, 30 Sep 2020 08:44:44 GMT

←Older revision		Revision as of 08:44, 30 September 2020
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	==TNA polymerase binary complex with primer/template duplex==		==TNA polymerase binary complex with primer/template duplex==
-	<StructureSection load='5vu6' size='340' side='right' caption='[[5vu6]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5vu6' size='340' side='right'caption='[[5vu6]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vu6]] 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=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VU6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vu6]] 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=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VU6 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu7\|5vu7]], [[5vu8\|5vu8]], [[5vu9\|5vu9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu7\|5vu7]], [[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=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [http://pdbe.org/5vu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 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=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [http://pdbe.org/5vu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5vu6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vu6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	[[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 07:33:09 GMT

←Older revision		Revision as of 07:33, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5vu6' size='340' side='right' caption='[[5vu6]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5vu6' size='340' side='right' caption='[[5vu6]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vu6]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vu6]] 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=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU6 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu7\|5vu7]], [[5vu8\|5vu8]], [[5vu9\|5vu9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu7\|5vu7]], [[5vu8\|5vu8]], [[5vu9\|5vu9]]</td></tr>
Line 9:		Line 9:
	<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=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [http://pdbe.org/5vu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 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=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [http://pdbe.org/5vu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 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 5vu6" 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 07:16:28 GMT

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

-	~~The entry~~ 5vu6 is ~~ON HOLD until Paper Publication~~	+	==TNA polymerase binary complex with primer/template duplex==
-		+	<StructureSection load='5vu6' size='340' side='right' caption='[[5vu6]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~: ~~Chim~~, N., ~~Chaput~~, J.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vu6]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU6 FirstGlance]. <br>
-	~~Description~~: ~~TNA~~ polymerase ~~binary complex with primer/template duplex~~	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vu5\|5vu5]], [[5vu7\|5vu7]], [[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=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [http://pdbe.org/5vu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 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 14:13:40 GMT

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

-	The entry 5vu6 is ON HOLD	+	The entry 5vu6 is ON HOLD until Paper Publication

	Authors: Chim, N., Chaput, J.C.		Authors: Chim, N., Chaput, J.C.
Line 7:		Line 7:
	Description: TNA polymerase binary complex with primer/template duplex		Description: TNA polymerase binary complex with primer/template duplex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chaput, J.C]]
	[[Category: Chim, N]]		[[Category: Chim, N]]
		+	[[Category: Chaput, J.C]]

OCA: Protected "5vu6" [edit=sysop:move=sysop]

OCA — Wed, 24 May 2017 11:50:48 GMT

Protected "5vu6" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:50, 24 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vu6 is ON HOLD Authors: Chim, N., Chaput, J.C. Description: TNA polymerase binary complex with primer/template duplex [[Category: Unreleased Struc...

OCA — Wed, 24 May 2017 11:50:47 GMT

New page: '''Unreleased structure''' The entry 5vu6 is ON HOLD Authors: Chim, N., Chaput, J.C. Description: TNA polymerase binary complex with primer/template duplex [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5vu6 is ON HOLD

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

Description: TNA polymerase binary complex with primer/template duplex
[[Category: Unreleased Structures]]
[[Category: Chaput, J.C]]
[[Category: Chim, N]]