6q4u - Revision history

OCA at 11:52, 24 January 2024

OCA — Wed, 24 Jan 2024 11:52:56 GMT

←Older revision		Revision as of 11:52, 24 January 2024
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	<StructureSection load='6q4u' size='340' side='right'caption='[[6q4u]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6q4u' size='340' side='right'caption='[[6q4u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q4u]] 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=6Q4U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6Q4U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q4u]] 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=6Q4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q4U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHZ:[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>HHZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.005Å</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=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHZ:[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>HHZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, pol1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=6q4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q4u OCA], [https://pdbe.org/6q4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q4u RCSB], [https://www.ebi.ac.uk/pdbsum/6q4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q4u ProSAT]</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=6q4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q4u OCA], [~~http~~://pdbe.org/6q4u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6q4u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6q4u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6q4u ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25104]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Diederichs, K~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Kropp, H M~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: ~~Marx, A~~]]	+	[[Category: Diederichs K]]
-	[[Category: ~~Dna binding protein~~]]	+	[[Category: Kropp HM]]
-	[[Category: ~~Dna polymerase archaeal b-family modified nucleotide next-generation sequencing~~]]	+	[[Category: Marx A]]

OCA at 17:31, 14 August 2019

OCA — Wed, 14 Aug 2019 17:31:08 GMT

←Older revision		Revision as of 17:31, 14 August 2019
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6q4u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6q4u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:32, 20 March 2019

OCA — Wed, 20 Mar 2019 08:32:26 GMT

←Older revision		Revision as of 08:32, 20 March 2019
Line 1:		Line 1:

	==KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP==		==KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP==
-	<StructureSection load='6q4u' size='340' side='right' caption='[[6q4u]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='6q4u' size='340' side='right'caption='[[6q4u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q4u]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q4U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q4u]] 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=6Q4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q4U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHZ:[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>HHZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHZ:[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>HHZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, pol1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=6q4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q4u OCA], [http://pdbe.org/6q4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q4u RCSB], [http://www.ebi.ac.uk/pdbsum/6q4u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q4u 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=6q4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q4u OCA], [http://pdbe.org/6q4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q4u RCSB], [http://www.ebi.ac.uk/pdbsum/6q4u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q4u ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]
	[[Category: Kropp, H M]]		[[Category: Kropp, H M]]

OCA at 15:33, 27 February 2019

OCA — Wed, 27 Feb 2019 15:33:51 GMT

←Older revision		Revision as of 15:33, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6q4u is ~~ON HOLD until Paper~~ Publication	+	==KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP==
		+	<StructureSection load='6q4u' size='340' side='right' caption='[[6q4u]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6q4u]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q4U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHZ:[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>HHZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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='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=6q4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q4u OCA], [http://pdbe.org/6q4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q4u RCSB], [http://www.ebi.ac.uk/pdbsum/6q4u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q4u ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Archaeal B-family DNA polymerases (DNA pols) are the driving force of cutting edge biotechnological applications like next-generation sequencing. The acceptance of chemically modified nucleotides by the DNA pols is key to these technologies. By now, no structural data are available for these DNA pols in complex with modified substrates which could build the basis for understanding interactions between the enzyme and the chemical modification and for further development of next generation nucleotides. For the first time we crystallized an exonuclease deficient variant of B-family KOD DNA pol wild-type with a modified nucleotide in a closed, ternary complex. We also crystalized the A-family DNA pol KlenTaq with the same nucleotide. The reported structural data elucidates how the protein and the DNA modulate two distinct conformations of the modification in the A- and B-family DNA pols and how these influence the processing of the modified nucleotide. Overall, this study provides first insights on how B-family DNA pols interplay with relevant modified substrates.

-	~~Authors: Kropp~~, H~~.M.~~, Diederichs, K.~~, Marx, A~~.	+	Structure of an archaeal B-family DNA polymerase in complex with a chemically modified nucleotide.,Marx A, Kropp H, Diederichs K Angew Chem Int Ed Engl. 2019 Feb 14. doi: 10.1002/anie.201900315. PMID:30761722<ref>PMID:30761722</ref>

-	~~Description: KlenTaq DNA pol in~~ a ~~closed ternary complex with 7~~-~~deaza~~-~~7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6q4u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]
-	[[Category: Kropp, H.M]]	+	[[Category: Kropp, H M]]
	[[Category: Marx, A]]		[[Category: Marx, A]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna polymerase archaeal b-family modified nucleotide next-generation sequencing]]

OCA at 06:53, 26 December 2018

OCA — Wed, 26 Dec 2018 06:53:28 GMT

←Older revision		Revision as of 06:53, 26 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6q4u is ON HOLD	+	The entry 6q4u is ON HOLD until Paper Publication

	Authors: Kropp, H.M., Diederichs, K., Marx, A.		Authors: Kropp, H.M., Diederichs, K., Marx, A.

OCA: Protected "6q4u" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2018 05:35:09 GMT

Protected "6q4u" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:35, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6q4u is ON HOLD Authors: Kropp, H.M., Diederichs, K., Marx, A. Description: KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydrox...

OCA — Wed, 12 Dec 2018 05:35:08 GMT

New page: '''Unreleased structure''' The entry 6q4u is ON HOLD Authors: Kropp, H.M., Diederichs, K., Marx, A. Description: KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydrox...

New page

'''Unreleased structure'''

The entry 6q4u is ON HOLD

Authors: Kropp, H.M., Diederichs, K., Marx, A.

Description: KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP
[[Category: Unreleased Structures]]
[[Category: Diederichs, K]]
[[Category: Kropp, H.M]]
[[Category: Marx, A]]