5yur - Revision history

OCA at 08:38, 22 November 2023

OCA — Wed, 22 Nov 2023 08:38:19 GMT

←Older revision		Revision as of 08:38, 22 November 2023
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	<StructureSection load='5yur' size='340' side='right'caption='[[5yur]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='5yur' size='340' side='right'caption='[[5yur]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yur]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YUR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yur]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YUR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~, ~~<scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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]] 2.035Å</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></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=5yur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yur OCA], [~~http~~://pdbe.org/5yur PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yur RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yur PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yur 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=5yur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yur OCA], [https://pdbe.org/5yur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yur RCSB], [https://www.ebi.ac.uk/pdbsum/5yur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yur ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>	+	[https://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>
	<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: ~~DNA~~-~~directed DNA polymerase~~]]	+	[[Category: Escherichia coli]]
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kottur, J]]	+	[[Category: Kottur J]]
-	[[Category: Nair~~, D T]]~~	+	[[Category: Nair DT]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna polymerase~~]]	+

OCA at 09:28, 21 October 2020

OCA — Wed, 21 Oct 2020 09:28:30 GMT

←Older revision		Revision as of 09:28, 21 October 2020
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	==DNA polymerase IV - DNA ternary complex 1==		==DNA polymerase IV - DNA ternary complex 1==
-	<StructureSection load='5yur' size='340' side='right' caption='[[5yur]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='5yur' size='340' side='right'caption='[[5yur]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yur]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YUR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yur]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YUR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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='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=5yur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yur OCA], [http://pdbe.org/5yur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yur RCSB], [http://www.ebi.ac.uk/pdbsum/5yur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yur 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=5yur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yur OCA], [http://pdbe.org/5yur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yur RCSB], [http://www.ebi.ac.uk/pdbsum/5yur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yur ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5yur" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yur" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Kottur, J]]		[[Category: Kottur, J]]
	[[Category: Nair, D T]]		[[Category: Nair, D T]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]

OCA at 07:20, 29 August 2018

OCA — Wed, 29 Aug 2018 07:20:19 GMT

←Older revision		Revision as of 07:20, 29 August 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yur is ~~ON HOLD~~	+	==DNA polymerase IV - DNA ternary complex 1==
		+	<StructureSection load='5yur' size='340' side='right' caption='[[5yur]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yur]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YUR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=5yur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yur OCA], [http://pdbe.org/5yur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yur RCSB], [http://www.ebi.ac.uk/pdbsum/5yur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yur ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA synthesis by DNA polymerases (dPols) is central to duplication and maintenance of the genome in all living organisms. dPols catalyze the formation of a phosphodiester bond between the incoming deoxynucleoside triphosphate and the terminal primer nucleotide with the release of a pyrophosphate (PPi) group. It is believed that formation of the phosphodiester bond is an endergonic reaction and PPi has to be hydrolyzed by accompanying pyrophosphatase enzymes to ensure that the free energy change of the DNA synthesis reaction is negative and it can proceed in the forward direction. The fact that DNA synthesis proceeds in vitro in the absence of pyrophosphatases represents a long-standing conundrum regarding the thermodynamics of the DNA synthesis reaction. Using time-resolved crystallography, we show that hydrolysis of PPi is an intrinsic and critical step of the DNA synthesis reaction catalyzed by dPols. The hydrolysis of PPi occurs after the formation of the phosphodiester bond and ensures that the DNA synthesis reaction is energetically favorable without the need for additional enzymes. Also, we observe that DNA synthesis is a two Mg2+ ion assisted stepwise associative SN2 reaction. Overall, this study provides deep temporal insight regarding the primary enzymatic reaction responsible for genome duplication.

-	~~Authors~~:	+	Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction.,Kottur J, Nair DT Nucleic Acids Res. 2018 Jul 6;46(12):5875-5885. doi: 10.1093/nar/gky402. PMID:29850882<ref>PMID:29850882</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yur" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Kottur, J]]
		+	[[Category: Nair, D T]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna polymerase]]

OCA at 04:32, 22 August 2018

OCA — Wed, 22 Aug 2018 04:32:04 GMT

←Older revision		Revision as of 04:32, 22 August 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yur is ON HOLD ~~until Paper Publication~~	+	The entry 5yur is ON HOLD

	Authors:		Authors:

OCA at 05:39, 25 July 2018

OCA — Wed, 25 Jul 2018 05:39:16 GMT

←Older revision		Revision as of 05:39, 25 July 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 05:04, 18 July 2018

OCA — Wed, 18 Jul 2018 05:04:10 GMT

←Older revision		Revision as of 05:04, 18 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yur is ON HOLD ~~until Paper Publication~~	+	The entry 5yur is ON HOLD

	Authors:		Authors:

OCA at 05:28, 4 July 2018

OCA — Wed, 04 Jul 2018 05:28:26 GMT

←Older revision		Revision as of 05:28, 4 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 03:47, 20 June 2018

OCA — Wed, 20 Jun 2018 03:47:59 GMT

←Older revision		Revision as of 03:47, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yur is ON HOLD ~~until Paper Publication~~	+	The entry 5yur is ON HOLD

	Authors:		Authors:

OCA at 04:56, 14 March 2018

OCA — Wed, 14 Mar 2018 04:56:49 GMT

←Older revision		Revision as of 04:56, 14 March 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 29 Nov 2017 05:00:35 GMT

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

←Older revision

Revision as of 05:00, 29 November 2017