5ijl - Revision history

OCA at 13:57, 30 August 2023

OCA — Wed, 30 Aug 2023 13:57:29 GMT

←Older revision		Revision as of 13:57, 30 August 2023
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	<StructureSection load='5ijl' size='340' side='right'caption='[[5ijl]], [[Resolution\|resolution]] 2.19Å' scene=''>		<StructureSection load='5ijl' size='340' side='right'caption='[[5ijl]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ijl]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrab Pyrab~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IJL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IJL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ijl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IJL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.19Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~polC, PYRAB01200, PAB2404 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=272844 PYRAB])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ijl OCA], [~~http~~://pdbe.org/5ijl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ijl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ijl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ijl 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=5ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ijl OCA], [https://pdbe.org/5ijl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ijl RCSB], [https://www.ebi.ac.uk/pdbsum/5ijl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ijl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DP2L_PYRAB DP2L_PYRAB]] Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity).	+	[https://www.uniprot.org/uniprot/DP2L_PYRAB DP2L_PYRAB] Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrab~~]]	+	[[Category: Pyrococcus abyssi GE5]]
-	[[Category: Larue, M De]]	+	[[Category: De Larue M]]
-	[[Category: Raia, P]]	+	[[Category: Raia P]]
-	[[Category: Sauguet, L]]	+	[[Category: Sauguet L]]
-	~~[[Category: Dna polymerase d-family]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:21, 3 June 2020

OCA — Wed, 03 Jun 2020 07:21:13 GMT

←Older revision		Revision as of 07:21, 3 June 2020
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	==D-family DNA polymerase - DP2 subunit (catalytic subunit)==		==D-family DNA polymerase - DP2 subunit (catalytic subunit)==
-	<StructureSection load='5ijl' size='340' side='right' caption='[[5ijl]], [[Resolution\|resolution]] 2.19Å' scene=''>	+	<StructureSection load='5ijl' size='340' side='right'caption='[[5ijl]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ijl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IJL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IJL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ijl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IJL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IJL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ijl OCA], [http://pdbe.org/5ijl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ijl RCSB], [http://www.ebi.ac.uk/pdbsum/5ijl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ijl ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polC, PYRAB01200, PAB2404 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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=5ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ijl OCA], [http://pdbe.org/5ijl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ijl RCSB], [http://www.ebi.ac.uk/pdbsum/5ijl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ijl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5ijl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ijl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrab]]
	[[Category: Larue, M De]]		[[Category: Larue, M De]]
	[[Category: Raia, P]]		[[Category: Raia, P]]

OCA at 05:32, 9 September 2016

OCA — Fri, 09 Sep 2016 05:32:28 GMT

←Older revision		Revision as of 05:32, 9 September 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5ijl is ~~ON HOLD~~	+	==D-family DNA polymerase - DP2 subunit (catalytic subunit)==
		+	<StructureSection load='5ijl' size='340' side='right' caption='[[5ijl]], [[Resolution\|resolution]] 2.19Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ijl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IJL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IJL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ijl OCA], [http://pdbe.org/5ijl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ijl RCSB], [http://www.ebi.ac.uk/pdbsum/5ijl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ijl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DP2L_PYRAB DP2L_PYRAB]] Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 A resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same 'double-psi beta-barrel' architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs.

-	~~Authors: Sauguet~~, L., Raia, P., ~~De Larue~~, M.	+	Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.,Sauguet L, Raia P, Henneke G, Delarue M Nat Commun. 2016 Aug 22;7:12227. doi: 10.1038/ncomms12227. PMID:27548043<ref>PMID:27548043</ref>

-	~~Description: D~~-~~family DNA polymerase~~ -~~DP2 subunit (catalytic subunit)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Sauguet, L]]~~	+	<div class="pdbe-citations 5ijl" style="background-color:#fffaf0;"></div>
-	[[Category: De Larue, M]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Larue, M De]]
	[[Category: Raia, P]]		[[Category: Raia, P]]
		+	[[Category: Sauguet, L]]
		+	[[Category: Dna polymerase d-family]]
		+	[[Category: Transferase]]

OCA at 22:32, 12 July 2016

OCA — Tue, 12 Jul 2016 22:32:06 GMT

←Older revision		Revision as of 22:32, 12 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Sauguet, L., Raia, P., De Larue, M.		Authors: Sauguet, L., Raia, P., De Larue, M.

OCA at 00:33, 11 May 2016

OCA — Wed, 11 May 2016 00:33:09 GMT

←Older revision		Revision as of 00:33, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Sauguet, L., Raia, P., De Larue, M.		Authors: Sauguet, L., Raia, P., De Larue, M.

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

OCA — Thu, 10 Mar 2016 02:26:44 GMT

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

←Older revision

Revision as of 02:26, 10 March 2016

OCA: New page: '''Unreleased structure''' The entry 5ijl is ON HOLD Authors: Sauguet, L., Raia, P., De Larue, M. Description: D-family DNA polymerase -DP2 subunit (catalytic subunit) [[Category: Unre...

OCA — Thu, 10 Mar 2016 02:26:43 GMT

New page: '''Unreleased structure''' The entry 5ijl is ON HOLD Authors: Sauguet, L., Raia, P., De Larue, M. Description: D-family DNA polymerase -DP2 subunit (catalytic subunit) [[Category: Unre...

New page

'''Unreleased structure'''

The entry 5ijl is ON HOLD

Authors: Sauguet, L., Raia, P., De Larue, M.

Description: D-family DNA polymerase -DP2 subunit (catalytic subunit)
[[Category: Unreleased Structures]]
[[Category: Sauguet, L]]
[[Category: De Larue, M]]
[[Category: Raia, P]]