6isi - Revision history

OCA at 09:52, 22 November 2023

OCA — Wed, 22 Nov 2023 09:52:30 GMT

←Older revision		Revision as of 09:52, 22 November 2023
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	<StructureSection load='6isi' size='340' side='right'caption='[[6isi]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6isi' size='340' side='right'caption='[[6isi]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6isi]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ISI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ISI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6isi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_sp._9oN-7 Thermococcus sp. 9oN-7] 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=6ISI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ISI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B0U:3-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]propanoic+acid'>B0U</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 3.2Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B0U:3-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]propanoic+acid'>B0U</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></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=6isi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6isi OCA], [~~http~~://pdbe.org/6isi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6isi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6isi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6isi 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=6isi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6isi OCA], [https://pdbe.org/6isi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6isi RCSB], [https://www.ebi.ac.uk/pdbsum/6isi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6isi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPOL_THES9 DPOL_THES9]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6isi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6isi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chang, W H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Linwu, S W~~]]	+	[[Category: Thermococcus sp. 9oN-7]]
-	[[Category: ~~Maestre-Reyna, M~~]]	+	[[Category: Chang WH]]
-	[[Category: ~~Tsai,~~ M D]]	+	[[Category: Linwu SW]]
-	[[Category: ~~Tu, Y H~~]]	+	[[Category: Maestre-Reyna M]]
-	[[Category: ~~Transferase-dna complex~~]]	+	[[Category: Tsai MD]]
		+	[[Category: Tu YH]]

OCA at 15:27, 28 August 2019

OCA — Wed, 28 Aug 2019 15:27:06 GMT

←Older revision		Revision as of 15:27, 28 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6isi is ~~ON HOLD until Paper~~ Publication	+	==Structure of 9N-I DNA polymerase incorporation with 3'-CL in the active site==
		+	<StructureSection load='6isi' size='340' side='right'caption='[[6isi]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6isi]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ISI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ISI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B0U:3-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]propanoic+acid'>B0U</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6isi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6isi OCA], [http://pdbe.org/6isi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6isi RCSB], [http://www.ebi.ac.uk/pdbsum/6isi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6isi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	It was reported in 1995 that T7 and Taq DNA polymerases possess 3'-esterase activity, but without follow-up studies. Here we report that the 3'-esterase activity is intrinsic to the Thermococcus sp. 9 degrees N DNA polymerase, and that it can be developed into a continuous method for DNA sequencing with dNTP analogs carrying a 3'-ester with a fluorophore. We first show that 3'-esterified dNTP can be incorporated into a template-primer DNA, and solve the crystal structures of the reaction intermediates and products. Then we show that the reaction can occur continuously, modulated by active site residues Tyr409 and Asp542. Finally, we use 5'-FAM-labeled primer and esterified dNTP with a dye to show that the reaction can proceed to ca. 450 base pairs, and that the intermediates of many individual steps can be identified. The results demonstrate the feasibility of a 3'-editing based DNA sequencing method that could find practical applications after further optimization.

-	~~Authors: Linwu, S~~.W., Maestre-Reyna, M., ~~Tsai~~, ~~M.D.~~, Tu, ~~Y.H.~~, Chang, W.H.	+	Thermococcus sp. 9 degrees N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.,LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD Commun Biol. 2019 Jun 20;2:224. doi: 10.1038/s42003-019-0458-7. eCollection 2019. PMID:31240262<ref>PMID:31240262</ref>

-	~~Description: Structure~~ of 9N-~~I DNA polymerase incorporation with 3'~~-~~CL in the active site~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Chang, W.H~~]]	+	<div class="pdbe-citations 6isi" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Linwu~~, S.W]]	+	== References ==
-	[[Category: ~~Tsai~~, ~~M.D]]~~	+	<references/>
-	~~[[Category: Tu, Y.H~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Chang, W H]]
		+	[[Category: Linwu, S W]]
	[[Category: Maestre-Reyna, M]]		[[Category: Maestre-Reyna, M]]
		+	[[Category: Tsai, M D]]
		+	[[Category: Tu, Y H]]
		+	[[Category: Transferase-dna complex]]

OCA at 06:01, 30 January 2019

OCA — Wed, 30 Jan 2019 06:01:15 GMT

←Older revision		Revision as of 06:01, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6isi is ON HOLD	+	The entry 6isi is ON HOLD until Paper Publication

	Authors: Linwu, S.W., Maestre-Reyna, M., Tsai, M.D., Tu, Y.H., Chang, W.H.		Authors: Linwu, S.W., Maestre-Reyna, M., Tsai, M.D., Tu, Y.H., Chang, W.H.
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	Description: Structure of 9N-I DNA polymerase incorporation with 3'-CL in the active site		Description: Structure of 9N-I DNA polymerase incorporation with 3'-CL in the active site
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Tsai, M.D]]
-	[[Category: Maestre-Reyna, M]]
	[[Category: Chang, W.H]]		[[Category: Chang, W.H]]
	[[Category: Linwu, S.W]]		[[Category: Linwu, S.W]]
		+	[[Category: Tsai, M.D]]
	[[Category: Tu, Y.H]]		[[Category: Tu, Y.H]]
		+	[[Category: Maestre-Reyna, M]]

OCA: Protected "6isi" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 18:55:54 GMT

Protected "6isi" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:55, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6isi is ON HOLD Authors: Linwu, S.W., Maestre-Reyna, M., Tsai, M.D., Tu, Y.H., Chang, W.H. Description: Structure of 9N-I DNA polymerase incorporat...

OCA — Sun, 02 Dec 2018 18:55:53 GMT

New page: '''Unreleased structure''' The entry 6isi is ON HOLD Authors: Linwu, S.W., Maestre-Reyna, M., Tsai, M.D., Tu, Y.H., Chang, W.H. Description: Structure of 9N-I DNA polymerase incorporat...

New page

'''Unreleased structure'''

The entry 6isi is ON HOLD

Authors: Linwu, S.W., Maestre-Reyna, M., Tsai, M.D., Tu, Y.H., Chang, W.H.

Description: Structure of 9N-I DNA polymerase incorporation with 3'-CL in the active site
[[Category: Unreleased Structures]]
[[Category: Tsai, M.D]]
[[Category: Maestre-Reyna, M]]
[[Category: Chang, W.H]]
[[Category: Linwu, S.W]]
[[Category: Tu, Y.H]]