3f2b - Revision history

OCA at 00:28, 28 December 2023

2023-12-28T00:28:06Z

← Older revision		Revision as of 00:28, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='3f2b' size='340' side='right'caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='3f2b' size='340' side='right'caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_kaustophilus"_prickett_1928 "bacillus~~ kaustophilus~~" prickett 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F2B FirstGlance]. <br>		<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F2B FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DGT:2-DEOXYGUANOSINE~~-~~5-TRIPHOSPHATE'>DGT</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.39Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3f2c\|3f2c]], [[3f2d\|3f2d]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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">GK1258~~, ~~polC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])~~<~~/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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [https://pdbe.org/3f2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [https://www.ebi.ac.uk/pdbsum/3f2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2b 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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [https://pdbe.org/3f2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [https://www.ebi.ac.uk/pdbsum/3f2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/Q5L0J3_GEOKA Q5L0J3_GEOKA]] Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).[HAMAP-Rule:MF_00356][SAAS:SAAS029460_004_008054]		[https://www.uniprot.org/uniprot/Q5L0J3_GEOKA Q5L0J3_GEOKA] Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).[HAMAP-Rule:MF_00356][SAAS:SAAS029460_004_008054]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3f2b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3f2b" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ kaustophilus ~~prickett 1928]]~~		[[Category: Geobacillus kaustophilus]]
	~~[[Category: DNA-directed DNA polymerase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bullard~~, J M~~]]		[[Category: Bullard JM]]
	[[Category: Christensen, J]]		[[Category: Christensen J]]
	[[Category: Davies~~, D R~~]]		[[Category: Davies DR]]
	[[Category: Evans~~, R J~~]]		[[Category: Evans RJ]]
	[[Category: Green~~, L S~~]]		[[Category: Green LS]]
	[[Category: Guiles~~, J W~~]]		[[Category: Guiles JW]]
	[[Category: Janjic, N]]		[[Category: Janjic N]]
	[[Category: Jarvis~~, T C~~]]		[[Category: Jarvis TC]]
	[[Category: Ribble~~, W K]]~~		[[Category: Ribble WK]]
	~~[[Category: Dna polymerase c]]~~
	~~[[Category: Dna polymerase iii]]~~
	~~[[Category: Dna replication]]~~
	~~[[Category: Dna-directed dna polymerase]]~~
	~~[[Category: Exonuclease]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Nuclease]]~~
	~~[[Category: Nucleotidyltransferase]]~~
	~~[[Category: Protein-dna complex]]~~
	~~[[Category: Replicative dna polymerase]]~~
	~~[[Category: Ternary complex]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Transferase-dna complex~~]]

OCA at 09:21, 23 February 2022

2022-02-23T09:21:59Z

← Older revision		Revision as of 09:21, 23 February 2022
Line 1:		Line 1:

	==DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn==		==DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn==
	<StructureSection load='3f2b' size='340' side='right' caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='3f2b' size='340' side='right'caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3F2B FirstGlance]. <br>		<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F2B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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">[[3f2c\|3f2c]], [[3f2d\|3f2d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3f2c\|3f2c]], [[3f2d\|3f2d]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [~~http~~://pdbe.org/3f2b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3f2b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2b 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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [https://pdbe.org/3f2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [https://www.ebi.ac.uk/pdbsum/3f2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/Q5L0J3_GEOKA Q5L0J3_GEOKA]] Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).[HAMAP-Rule:MF_00356][SAAS:SAAS029460_004_008054]		[[https://www.uniprot.org/uniprot/Q5L0J3_GEOKA Q5L0J3_GEOKA]] Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).[HAMAP-Rule:MF_00356][SAAS:SAAS029460_004_008054]
	== 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/f2/3f2b_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f2/3f2b_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: Bacillus kaustophilus prickett 1928]]		[[Category: Bacillus kaustophilus prickett 1928]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
			[[Category: Large Structures]]
	[[Category: Bullard, J M]]		[[Category: Bullard, J M]]
	[[Category: Christensen, J]]		[[Category: Christensen, J]]

OCA at 05:08, 16 November 2017

2017-11-16T05:08:53Z

← Older revision		Revision as of 05:08, 16 November 2017
Line 1:		Line 1:

	==DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn==		==DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn==
	<StructureSection load='3f2b' size='340' side='right' caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='3f2b' size='340' side='right' caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://pdbe.org/3f2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b 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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://pdbe.org/3f2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3f2b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3f2b" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:00, 8 February 2016

2016-02-08T10:00:03Z

← Older revision		Revision as of 10:00, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3f2b' size='340' side='right' caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='3f2b' size='340' side='right' caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_kaustophilus Geobacillus~~ kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2B FirstGlance]. <br>		<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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">[[3f2c\|3f2c]], [[3f2d\|3f2d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f2c\|3f2c]], [[3f2d\|3f2d]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 ~~Geobacillus~~ kaustophilus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b 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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://pdbe.org/3f2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3f2b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3f2b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacillus kaustophilus prickett 1928]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	~~[[Category: Geobacillus kaustophilus]]~~
	[[Category: Bullard, J M]]		[[Category: Bullard, J M]]
	[[Category: Christensen, J]]		[[Category: Christensen, J]]

OCA at 22:31, 24 December 2014

2014-12-24T22:31:08Z

← Older revision		Revision as of 22:31, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2B FirstGlance]. <br>		<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2B FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f2c\|3f2c]], [[3f2d\|3f2d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f2c\|3f2c]], [[3f2d\|3f2d]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b 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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q5L0J3_GEOKA Q5L0J3_GEOKA]] Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).[HAMAP-Rule:MF_00356][SAAS:SAAS029460_004_008054]
	== 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: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]
	[[Category: Bullard, J M.]]		[[Category: Bullard, J M]]
	[[Category: Christensen, J.]]		[[Category: Christensen, J]]
	[[Category: Davies, D R.]]		[[Category: Davies, D R]]
	[[Category: Evans, R J.]]		[[Category: Evans, R J]]
	[[Category: Green, L S.]]		[[Category: Green, L S]]
	[[Category: Guiles, J W.]]		[[Category: Guiles, J W]]
	[[Category: Janjic, N.]]		[[Category: Janjic, N]]
	[[Category: Jarvis, T C.]]		[[Category: Jarvis, T C]]
	[[Category: Ribble, W K.]]		[[Category: Ribble, W K]]
	[[Category: Dna polymerase c]]		[[Category: Dna polymerase c]]
	[[Category: Dna polymerase iii]]		[[Category: Dna polymerase iii]]

OCA at 11:14, 29 September 2014

2014-09-29T11:14:15Z

← Older revision		Revision as of 11:14, 29 September 2014
Line 1:		Line 1:
	[[Image:~~3f2b~~.~~png~~\|~~left~~\|~~200px~~]]		==DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn==
			<StructureSection load='3f2b' size='340' side='right' caption='[[3f2b]], [[Resolution\|resolution]] 2.39Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2B FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f2c\|3f2c]], [[3f2d\|3f2d]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b 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/f2/3f2b_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 ==
			PolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-A resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique beta-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a mechanism by which the active site can communicate with the rest of the replisome to trigger proofreading after nucleotide misincorporation, leading to an integrated model for controlling the dynamic switch between replicative and repair polymerases. This ternary complex of a cellular replicative polymerase affords insights into polymerase fidelity, evolution, and structural diversity.

	~~{{STRUCTURE_3f2b\| PDB=3f2b \| SCENE= }}~~		Structure of PolC reveals unique DNA binding and fidelity determinants.,Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20695-700. Epub 2008 Dec 23. PMID:19106298<ref>PMID:19106298</ref>

	~~===DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA~~, ~~dGTP, Mg and Zn===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19106298}}~~

	~~==About this Structure==~~
	~~[[3f2b]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA].~~

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:019106298<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]

OCA at 09:47, 20 October 2012

2012-10-20T09:47:15Z

← Older revision		Revision as of 09:47, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[3f2b]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA].		[[3f2b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA].

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

OCA: Protected "3f2b" [edit=sysop:move=sysop]

2012-07-25T23:57:19Z

Protected "3f2b" [edit=sysop:move=sysop]

← Older revision	Revision as of 23:57, 25 July 2012
(No difference)

OCA at 23:57, 25 July 2012

2012-07-25T23:57:18Z

← Older revision		Revision as of 23:57, 25 July 2012
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:3f2b.png\|left\|200px]]		[[Image:3f2b.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3f2b", 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.~~
	~~-->~~
	{{STRUCTURE_3f2b\| PDB=3f2b \| SCENE= }}		{{STRUCTURE_3f2b\| PDB=3f2b \| SCENE= }}

	===DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn===		===DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_19106298}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 19106298 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_19106298}}		{{ABSTRACT_PUBMED_19106298}}

	==About this Structure==		==About this Structure==
	~~3F2B~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA].		[[3f2b]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA].

			==See Also==
			*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~19106298~~</ref><references group="xtra"/>		<ref group="xtra">PMID:019106298</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]
Line 35:		Line 26:
	[[Category: Jarvis, T C.]]		[[Category: Jarvis, T C.]]
	[[Category: Ribble, W K.]]		[[Category: Ribble, W K.]]
	~~[[Category: Cytoplasm]]~~
	[[Category: Dna polymerase c]]		[[Category: Dna polymerase c]]
	[[Category: Dna polymerase iii]]		[[Category: Dna polymerase iii]]
Line 49:		Line 39:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 3 14:45:17 2010''~~

OCA at 12:45, 3 March 2010

2010-03-03T12:45:18Z

← Older revision		Revision as of 12:45, 3 March 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
	[[Image:3f2b.~~jpg~~\|left\|200px]]		[[Image:3f2b.png\|left\|200px]]

	<!--		<!--
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	3F2B is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA].		3F2B is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA].

	==Reference==		==Reference==
Line 48:		Line 48:
	[[Category: Ternary complex]]		[[Category: Ternary complex]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transferase/dna complex]]		[[Category: Transferase-dna complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jan 21 10~~:48:~~21 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 3 14:45:17 2010''