6mu4 - Revision history

OCA at 06:38, 11 October 2023

OCA — Wed, 11 Oct 2023 06:38:57 GMT

←Older revision		Revision as of 06:38, 11 October 2023
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	<StructureSection load='6mu4' size='340' side='right'caption='[[6mu4]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='6mu4' size='340' side='right'caption='[[6mu4]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mu4]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MU4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mu4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] 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=6MU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MU4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'~~>~~MG</scene>, <scene name='pdbligand=MPD:(4S)~~-~~2-METHYL-2~~,~~4-PENTANEDIOL'>MPD</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]] 1.62Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5L:9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE'>A5L</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE'>UF2</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5L:9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE'>A5L</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE'>UF2</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=6mu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mu4 OCA], [https://pdbe.org/6mu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mu4 RCSB], [https://www.ebi.ac.uk/pdbsum/6mu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mu4 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=6mu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mu4 OCA], [~~http~~://pdbe.org/6mu4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mu4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mu4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mu4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E1C9K5_GEOSE E1C9K5_GEOSE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980]]~~	+	[[Category: Geobacillus stearothermophilus]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chaput, J C~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Chim, N~~]]	+	[[Category: Chaput JC]]
-	[[Category: ~~Jackson, L~~ N]]	+	[[Category: Chim N]]
-	[[Category: ~~Transferase-dna complex]]~~	+	[[Category: Jackson LN]]
-	~~[[Category: Xna reverse transcription~~]]	+

OCA at 06:18, 7 August 2019

OCA — Wed, 07 Aug 2019 06:18:55 GMT

←Older revision		Revision as of 06:18, 7 August 2019
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	<StructureSection load='6mu4' size='340' side='right'caption='[[6mu4]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='6mu4' size='340' side='right'caption='[[6mu4]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mu4]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mu4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MU4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=A5L:9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE'>A5L</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE'>UF2</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5L:9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE'>A5L</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE'>UF2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=6mu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mu4 OCA], [http://pdbe.org/6mu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mu4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mu4 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=6mu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mu4 OCA], [http://pdbe.org/6mu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mu4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mu4 ProSAT]</span></td></tr>
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:32, 19 June 2019

OCA — Wed, 19 Jun 2019 06:32:12 GMT

←Older revision		Revision as of 06:32, 19 June 2019
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=6mu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mu4 OCA], [http://pdbe.org/6mu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mu4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mu4 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=6mu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mu4 OCA], [http://pdbe.org/6mu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mu4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mu4 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2'-deoxy-2'-fluoro-beta-d-arabino nucleic acid (FANA) and alpha-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.
		+
		+	Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase.,Jackson LN, Chim N, Shi C, Chaput JC Nucleic Acids Res. 2019 Jun 6. pii: 5512092. doi: 10.1093/nar/gkz513. PMID:31170294<ref>PMID:31170294</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mu4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 22:48, 5 June 2019

OCA — Wed, 05 Jun 2019 22:48:26 GMT

←Older revision		Revision as of 22:48, 5 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mu4 is ~~ON HOLD until Paper Publication~~	+	==Bst DNA polymerase I FANA/DNA binary complex==
-		+	<StructureSection load='6mu4' size='340' side='right'caption='[[6mu4]], [[Resolution\|resolution]] 1.62Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mu4]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MU4 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=A5L:9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE'>A5L</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE'>UF2</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=6mu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mu4 OCA], [http://pdbe.org/6mu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mu4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mu4 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Chaput, J C]]
		+	[[Category: Chim, N]]
		+	[[Category: Jackson, L N]]
		+	[[Category: Transferase-dna complex]]
		+	[[Category: Xna reverse transcription]]

OCA at 10:50, 7 November 2018

OCA — Wed, 07 Nov 2018 10:50:05 GMT

←Older revision		Revision as of 10:50, 7 November 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6mu4 is ON HOLD	+	The entry 6mu4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6mu4" [edit=sysop:move=sysop]

OCA — Wed, 31 Oct 2018 05:33:02 GMT

Protected "6mu4" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:33, 31 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mu4 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 31 Oct 2018 05:33:00 GMT

New page: '''Unreleased structure''' The entry 6mu4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6mu4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]