8ica - Revision history

OCA at 11:12, 2 August 2023

2023-08-02T11:12:49Z

←Older revision		Revision as of 11:12, 2 August 2023
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		+
	==DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)==		==DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)==
-	<StructureSection load='8ica' size='340' side='right' caption='[[8ica]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='8ica' size='340' side='right'caption='[[8ica]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[8ica]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=8ICA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8ica]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ICA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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">[[7ice\|7ice]], [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=8ica FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ica OCA], [~~http~~://pdbe.org/8ica PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=8ica RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/8ica PDBsum]</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=8ica FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ica OCA], [https://pdbe.org/8ica PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ica RCSB], [https://www.ebi.ac.uk/pdbsum/8ica PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ica ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>	+	[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	== 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/ic/8ica_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/8ica_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>
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	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Pelletier, H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Sawaya, M R~~]]	+	[[Category: Pelletier H]]
-	[[Category: ~~Dna repair]]~~	+	[[Category: Sawaya MR]]
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 08:22, 10 February 2016

2016-02-10T08:22:55Z

←Older revision		Revision as of 08:22, 10 February 2016
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	<StructureSection load='8ica' size='340' side='right' caption='[[8ica]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='8ica' size='340' side='right' caption='[[8ica]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[8ica]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8ICA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8ica]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8ICA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</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=8ica FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ica OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8ica RCSB], [http://www.ebi.ac.uk/pdbsum/8ica 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=8ica FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ica OCA], [http://pdbe.org/8ica PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=8ica RCSB], [http://www.ebi.ac.uk/pdbsum/8ica PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	<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=8ica ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 8ica" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Pelletier, H]]		[[Category: Pelletier, H]]
	[[Category: Sawaya, M R]]		[[Category: Sawaya, M R]]

OCA at 08:36, 18 December 2014

2014-12-18T08:36:19Z

←Older revision		Revision as of 08:36, 18 December 2014
Line 1:		Line 1:
-	[[~~Image:~~8ica.~~png~~\|~~left~~\|200px]]	+	==DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)==
		+	<StructureSection load='8ica' size='340' side='right' caption='[[8ica]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8ica]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8ICA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</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=8ica FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ica OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8ica RCSB], [http://www.ebi.ac.uk/pdbsum/8ica 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/ic/8ica_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 ==
		+	X-ray crystallographic studies have shown that DNA binding by human polymerase beta (pol beta) occurs primarily through two structurally and sequentially homologous helix-hairpin-helix (HhH) motifs, one in the fingers subdomain and the other in the 8-kDa domain [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996a) Biochemistry 35, 12742-12761]. In that DNA binding by each HhH motif is facilitated by a metal ion, we set out to determine the identity of the metal ion that most likely binds to the HhH motif in vivo. Crystal soaking experiments were performed on human pol beta-DNA cocrystals with Mg2+, Ca2+, Na+, and K+, the four most prevalent metal ions in the cell, and in each case a data set was collected and the resulting structure was refined. Under the conditions tested, the HhH motifs of pol beta have an affinity for these biologically prevalent metal ions in the order Mg2+ < Ca2+ < Na+ < K+, with K+ displaying the strongest binding. Crystals soaked in the presence of Tl+, a commonly used spectroscopic probe for K+, were too X-ray-sensitive to establish the binding behavior of Tl+, but soaking experiments with Ba2+ and Cs+ resulted in relatively stable crystals that gave evidence of metal ion binding in both HhH motifs, confirming that larger monovalent and divalent metal ions are capable of binding to the HhH metal sites. Although Mn2+, which has been categorized as a potent polymerase mutagen, binds to the HhH motifs with a greater affinity than Mg2+, Mn2+ does not bind to the HhH motifs in the presence of equimolar concentrations of Na+. These results suggest that in vivo, where Mn2+ is present only in trace amounts, Mn2+ probably does not have a large effect on DNA binding and may instead manifest a mutagenic effect on pol beta primarily by distorting nucleotide binding or by directly affecting the catalytic step [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996b) Biochemistry 35, 12762-12777]. Crystal soaking experiments with 31-kDa apoenzyme crystals show that, in the absence of DNA, the HhH motif in the fingers subdomain binds metal ions with either much lower occupancy or not at all, indicating that metal ion binding is dependent on the presence of the DNA substrate.

-	~~{{STRUCTURE_8ica\| PDB=8ica \| SCENE= }}~~	+	Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.,Pelletier H, Sawaya MR Biochemistry. 1996 Oct 1;35(39):12778-87. PMID:8841120<ref>PMID:8841120</ref>

-	~~===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA~~; ~~SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8841120}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[8ica]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008841120<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Pelletier, H.]]	+	[[Category: Pelletier, H]]
-	[[Category: Sawaya, M R.]]	+	[[Category: Sawaya, M R]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
	[[Category: Dna replication]]		[[Category: Dna replication]]

OCA at 16:57, 20 October 2012

2012-10-20T16:57:15Z

←Older revision		Revision as of 16:57, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[8ica]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA].	+	[[8ica]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA].

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

OCA: Protected "8ica" [edit=sysop:move=sysop]

2012-07-26T23:21:39Z

Protected "8ica" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:21, 26 July 2012

OCA at 23:21, 26 July 2012

2012-07-26T23:21:38Z

←Older revision		Revision as of 23:21, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:8ica.png\|left\|200px]]		[[Image:8ica.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_8ica", 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_8ica\| PDB=8ica \| SCENE= }}		{{STRUCTURE_8ica\| PDB=8ica \| SCENE= }}

	===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)===		===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8841120}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8841120 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8841120}}		{{ABSTRACT_PUBMED_8841120}}

	==About this Structure==		==About this Structure==
-	~~8ICA~~ is a 3 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA].	+	[[8ica]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8841120~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008841120</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
Line 31:		Line 22:
	[[Category: Dna-directed dna polymerase]]		[[Category: Dna-directed dna polymerase]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
-		+	[[Category: Transferase-dna complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 16:48:14 2009''~~	+

OCA at 14:48, 17 February 2009

2009-02-17T14:48:15Z

←Older revision		Revision as of 14:48, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	8ICA is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA].	+	8ICA is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ICA OCA].

	==Reference==		==Reference==
-	~~Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis., Pelletier H, Sawaya MR, Biochemistry. 1996 Oct 1;35(39):12778-87.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/8841120 8841120]~~	+	<ref group="xtra">PMID:8841120</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Single protein]]
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
Line 33:		Line 32:
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri Jul 11 12~~:53:~~52 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:48:14 2009''

OCA at 09:53, 11 July 2008

2008-07-11T09:53:52Z

←Older revision		Revision as of 09:53, 11 July 2008
Line 1:		Line 1:
-	[[Image:8ica.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:8ica.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_8ica\| PDB=8ica \| SCENE= }}		{{STRUCTURE_8ica\| PDB=8ica \| SCENE= }}

-	~~'''~~DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)~~'''~~	+	===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)===


-	~~==Overview==~~	+	<!--
-	X-~~ray crystallographic studies have shown that DNA binding by human polymerase beta (pol beta) occurs primarily through two structurally and sequentially homologous helix~~-~~hairpin-helix (HhH) motifs~~, ~~one in the fingers subdomain and the other in the 8-kDa domain [Pelletier~~, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996a) Biochemistry 35, 12742-12761]. In that DNA binding by each HhH motif is facilitated by a metal ion, we set out to determine the identity of the ~~metal ion that most likely binds~~ to the ~~HhH motif in vivo. Crystal soaking experiments were performed~~ on ~~human pol beta-DNA cocrystals with Mg2+, Ca2+, Na+, and K+, the four most prevalent metal ions in the cell, and in each case a data set was collected and the resulting structure was refined~~. Under the conditions tested, the HhH motifs of pol beta have an affinity for these biologically prevalent metal ions in the order Mg2+ < Ca2+ < Na+ < K+, with K+ displaying the strongest binding. Crystals soaked in the presence of Tl+, a commonly used spectroscopic probe for K+, were too X-ray-sensitive to establish the binding behavior of Tl+, but soaking experiments with Ba2+ and Cs+ resulted in relatively stable crystals that gave evidence of metal ion binding in both HhH motifs, confirming that larger monovalent and divalent metal ions are capable of binding to the HhH metal sites. Although Mn2+, which has been categorized as a potent polymerase mutagen, binds to the HhH motifs with a greater affinity than Mg2+, Mn2+ does not bind to the HhH motifs in the presence of equimolar concentrations of Na+. These results suggest that in vivo, where ~~Mn2+~~ is present only in trace amounts, Mn2+ probably does not have a large effect on DNA binding and may instead manifest a mutagenic effect on pol beta primarily by distorting nucleotide binding or by directly affecting the ~~catalytic step [Pelletier, H~~.~~, Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996b) Biochemistry 35, 12762~~-~~12777]. Crystal soaking experiments with 31~~-kDa apoenzyme crystals show that, in the absence of DNA, the HhH motif in the fingers subdomain binds metal ions with either much lower occupancy or not at all, indicating that metal ion binding is dependent on the presence of the DNA substrate.	+	The line below this paragraph, {{ABSTRACT_PUBMED_8841120}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 8841120 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_8841120}}

	==About this Structure==		==About this Structure==
Line 28:		Line 32:
	[[Category: Dna-directed dna polymerase]]		[[Category: Dna-directed dna polymerase]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 22~~:49:37 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Jul 11 12:53:52 2008''

OCA at 19:49, 4 May 2008

2008-05-04T19:49:39Z

←Older revision		Revision as of 19:49, 4 May 2008
Line 1:		Line 1:
	[[Image:8ica.gif\|left\|200px]]		[[Image:8ica.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 8ica \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>8ica</scene>~~, ~~resolution 3~~.~~000Å~~	+	The line below this paragraph, containing "STRUCTURE_8ica", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'~~-~~DEOXYADENOSINE~~-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DTP:2'-DEOXYADENOSINE+5'-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_8ica\| PDB=8ica \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8ica FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ica OCA], [http://www.ebi.ac.uk/pdbsum/8ica PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=8ica RCSB]</span>	+
-	}}	+

	'''DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)'''		'''DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)'''
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	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
-	[[Category: ~~complex (nucleotidyltransferase/dna]]~~	+	[[Category: Dna repair]]
-	~~[[Category: dna~~ repair]]	+	[[Category: Dna replication]]
-	[[Category: ~~dna~~ replication]]	+	[[Category: Dna-directed dna polymerase]]
-	[[Category: ~~dna~~-directed dna polymerase]]	+	[[Category: Nucleotidyltransferase]]
-	[[Category: ~~nucleotidyltransferase~~]]	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:49:37 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:45:15 2008''	+

OCA at 02:45, 31 March 2008

2008-03-31T02:45:17Z

←Older revision		Revision as of 02:45, 31 March 2008
Line 4:		Line 4:
	\|PDB= 8ica \|SIZE=350\|CAPTION= <scene name='initialview01'>8ica</scene>, resolution 3.000Å		\|PDB= 8ica \|SIZE=350\|CAPTION= <scene name='initialview01'>8ica</scene>, resolution 3.000Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:~~SODIUM+ION~~'>NA</scene> ~~and~~ <scene name='pdbligand=DTP:2'-DEOXYADENOSINE 5'-TRIPHOSPHATE'>DTP</scene>	+	\|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DTP:2'-DEOXYADENOSINE+5'-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8ica FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ica OCA], [http://www.ebi.ac.uk/pdbsum/8ica PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=8ica RCSB]</span>
	}}		}}

Line 24:		Line 27:
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
-	[[Category: CA]]
-	[[Category: DTP]]
-	[[Category: NA]]
	[[Category: complex (nucleotidyltransferase/dna]]		[[Category: complex (nucleotidyltransferase/dna]]
	[[Category: dna repair]]		[[Category: dna repair]]
Line 33:		Line 33:
	[[Category: nucleotidyltransferase]]		[[Category: nucleotidyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun~~ Mar ~~23 16~~:06:44 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:45:15 2008''