2hpi - Revision history

OCA at 09:33, 14 February 2024

2024-02-14T09:33:51Z

←Older revision		Revision as of 09:33, 14 February 2024
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	<StructureSection load='2hpi' size='340' side='right'caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2hpi' size='340' side='right'caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HPI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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]] 3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2hpm\|2hpm]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~dnaE ([https://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~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [https://pdbe.org/2hpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [https://www.ebi.ac.uk/pdbsum/2hpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hpi 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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [https://pdbe.org/2hpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [https://www.ebi.ac.uk/pdbsum/2hpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hpi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPO3A_THEAQ DPO3A_THEAQ]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase (By similarity).	+	[https://www.uniprot.org/uniprot/DPO3A_THEAQ DPO3A_THEAQ] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2hpi ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2hpi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of Thermus aquaticus DNA polymerase III alpha subunit reveals that the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that of the eukaryotic replicative polymerase but rather belongs to the Polbeta-like nucleotidyltransferase superfamily. A model of the polymerase complexed with both DNA and beta-sliding clamp interacting with a reoriented binding domain and internal beta binding site was constructed that is consistent with existing biochemical data. Within the crystal, two C-terminal domains are interacting through a surface that is larger than many dimer interfaces. Since replicative polymerases of eubacteria and eukaryotes/archaea are not homologous, the nature of the replicative polymerase in the last common ancestor is unknown. Although other possibilities have been proposed, the plausibility of a ribozyme DNA polymerase should be considered.

-	The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.,Bailey S, Wing RA, Steitz TA Cell. 2006 Sep 8;126(5):893-904. PMID:16959569<ref>PMID:16959569</ref>	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 2hpi" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25104]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bailey, S~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: ~~Steitz, T A~~]]	+	[[Category: Bailey S]]
-	[[Category: ~~Wing, R A~~]]	+	[[Category: Steitz TA]]
-	[[Category: ~~Pol-beta-like nucleotidyltransferase fold]]~~	+	[[Category: Wing RA]]
-	~~[[Category: Transferase~~]]	+

OCA at 07:19, 24 March 2021

2021-03-24T07:19:21Z

←Older revision		Revision as of 07:19, 24 March 2021
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	==Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III==		==Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III==
-	<StructureSection load='2hpi' size='340' side='right' caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='2hpi' size='340' side='right'caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hpi]] is a 1 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=2HPI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HPI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hpm\|2hpm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hpm\|2hpm]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([https://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'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [~~http~~://pdbe.org/2hpi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hpi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hpi 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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [https://pdbe.org/2hpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [https://www.ebi.ac.uk/pdbsum/2hpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hpi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPO3A_THEAQ DPO3A_THEAQ]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase (By similarity).	+	[[https://www.uniprot.org/uniprot/DPO3A_THEAQ DPO3A_THEAQ]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hp/2hpi_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hp/2hpi_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 37:		Line 37:
	[[Category: Atcc 25104]]		[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Bailey, S]]		[[Category: Bailey, S]]
	[[Category: Steitz, T A]]		[[Category: Steitz, T A]]

OCA at 08:15, 18 October 2017

2017-10-18T08:15:08Z

←Older revision		Revision as of 08:15, 18 October 2017
Line 1:		Line 1:
		+
	==Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III==		==Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III==
	<StructureSection load='2hpi' size='340' side='right' caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2hpi' size='340' side='right' caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [http://pdbe.org/2hpi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [http://www.ebi.ac.uk/pdbsum/2hpi PDBsum]</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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [http://pdbe.org/2hpi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [http://www.ebi.ac.uk/pdbsum/2hpi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hpi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2hpi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hpi" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:27, 7 February 2016

2016-02-07T22:27:40Z

←Older revision		Revision as of 22:27, 7 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2hpi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:28, 10 September 2015

2015-09-10T05:28:03Z

←Older revision		Revision as of 05:28, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2hpi' size='340' side='right' caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2hpi' size='340' side='right' caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hpi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_aquaticus Thermus aquaticus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hpi]] is a 1 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=2HPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HPI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hpm\|2hpm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hpm\|2hpm]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ~~Thermus aquaticus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [http://www.ebi.ac.uk/pdbsum/2hpi PDBsum]</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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [http://pdbe.org/2hpi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [http://www.ebi.ac.uk/pdbsum/2hpi PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2hpi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Thermus aquaticus]]
	[[Category: Bailey, S]]		[[Category: Bailey, S]]
	[[Category: Steitz, T A]]		[[Category: Steitz, T A]]

OCA at 18:36, 24 December 2014

2014-12-24T18:36:18Z

←Older revision		Revision as of 18:36, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hpi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HPI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hpi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HPI FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hpm\|2hpm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hpm\|2hpm]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [http://www.ebi.ac.uk/pdbsum/2hpi PDBsum]</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=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [http://www.ebi.ac.uk/pdbsum/2hpi PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO3A_THEAQ DPO3A_THEAQ]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Bailey, S.]]	+	[[Category: Bailey, S]]
-	[[Category: Steitz, T A.]]	+	[[Category: Steitz, T A]]
-	[[Category: Wing, R A.]]	+	[[Category: Wing, R A]]
	[[Category: Pol-beta-like nucleotidyltransferase fold]]		[[Category: Pol-beta-like nucleotidyltransferase fold]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 03:24, 29 September 2014

2014-09-29T03:24:33Z

←Older revision		Revision as of 03:24, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2hpi.~~png~~\|~~left~~\|200px]]	+	==Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III==
		+	<StructureSection load='2hpi' size='340' side='right' caption='[[2hpi]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hpi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HPI FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hpm\|2hpm]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hpi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hpi RCSB], [http://www.ebi.ac.uk/pdbsum/2hpi PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hp/2hpi_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of Thermus aquaticus DNA polymerase III alpha subunit reveals that the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that of the eukaryotic replicative polymerase but rather belongs to the Polbeta-like nucleotidyltransferase superfamily. A model of the polymerase complexed with both DNA and beta-sliding clamp interacting with a reoriented binding domain and internal beta binding site was constructed that is consistent with existing biochemical data. Within the crystal, two C-terminal domains are interacting through a surface that is larger than many dimer interfaces. Since replicative polymerases of eubacteria and eukaryotes/archaea are not homologous, the nature of the replicative polymerase in the last common ancestor is unknown. Although other possibilities have been proposed, the plausibility of a ribozyme DNA polymerase should be considered.

-	~~{{STRUCTURE_2hpi\| PDB=2hpi \| SCENE= }}~~	+	The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.,Bailey S, Wing RA, Steitz TA Cell. 2006 Sep 8;126(5):893-904. PMID:16959569<ref>PMID:16959569</ref>

-	~~===Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure~~ of ~~DNA Polymerase III===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16959569}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2hpi]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_aquaticus Thermus aquaticus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016959569<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 08:01, 20 October 2012

2012-10-20T08:01:52Z

←Older revision		Revision as of 08:01, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2hpi]] is a 1 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA].	+	[[2hpi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA].

	==See Also==		==See Also==

OCA: Protected "2hpi" [edit=sysop:move=sysop]

2012-07-25T18:13:41Z

Protected "2hpi" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:13, 25 July 2012

OCA at 18:13, 25 July 2012

2012-07-25T18:13:40Z

←Older revision		Revision as of 18:13, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2hpi.png\|left\|200px]]		[[Image:2hpi.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2hpi", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_2hpi\| PDB=2hpi \| SCENE= }}		{{STRUCTURE_2hpi\| PDB=2hpi \| SCENE= }}

	===Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III===		===Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16959569}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16959569 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16959569}}		{{ABSTRACT_PUBMED_16959569}}

	==About this Structure==		==About this Structure==
-	~~2HPI~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA].	+	[[2hpi]] is a 1 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPI OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16959569~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016959569</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
Line 30:		Line 21:
	[[Category: Wing, R A.]]		[[Category: Wing, R A.]]
	[[Category: Pol-beta-like nucleotidyltransferase fold]]		[[Category: Pol-beta-like nucleotidyltransferase fold]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 16:53:28 2009''~~	+