3tab - Revision history

OCA at 10:07, 1 March 2024

2024-03-01T10:07:00Z

← Older revision		Revision as of 10:07, 1 March 2024
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	<StructureSection load='3tab' size='340' side='right'caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3tab' size='340' side='right'caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpr69 Bpr69~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAB FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.8Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OC:2-DEOXY-5-HYDROXYCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5OC</scene>~~</td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5OC:2-DEOXY-5-HYDROXYCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5OC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tae\|3tae]]~~, ~~[[3taf\|3taf]], [[3tag\|3tag]]~~<~~/div></td></tr>~~
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">43, gp43 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [https://pdbe.org/3tab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [https://www.ebi.ac.uk/pdbsum/3tab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tab 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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [https://pdbe.org/3tab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [https://www.ebi.ac.uk/pdbsum/3tab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.		[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	5-Hydroxycytosine (5-OHC) is a stable oxidation product of cytosine associated with an increased frequency of C --> T transition mutations. When this lesion escapes recognition by the base excision repair pathway and persists to serve as a templating base during DNA synthesis, replicative DNA polymerases often misincorporate dAMP at the primer terminus, which can lead to fixation of mutations and subsequent disease. To characterize the dynamics of DNA synthesis opposite 5-OHC, we initiated a comparison of unmodified dCMP to 5-OHC, 5-fluorocytosine (5-FC), and 5-methylcytosine (5-MEC) in which these bases act as templates in the active site of RB69 gp43, a high-fidelity DNA polymerase sharing homology with human replicative DNA polymerases. This study presents the first crystal structure of any DNA polymerase binding this physiologically important premutagenic DNA lesion, showing that while dGMP is stabilized by 5-OHC through normal Watson-Crick base pairing, incorporation of dAMP leads to unstacking and instability in the template. Furthermore, the electronegativity of the C5 substituent appears to be important in the miscoding potential of these cytosine-like templates. While dAMP is incorporated opposite 5-OHC approximately 5 times more efficiently than opposite unmodified dCMP, an elevated level of incorporation is also observed opposite 5-FC but not 5-MEC. Taken together, these data imply that the nonuniform templating by 5-OHC is due to weakened stacking capabilities, which allows dAMP incorporation to proceed in a manner similar to that observed opposite abasic sites.

	The Miscoding Potential of 5-Hydroxycytosine Arises Due to Template Instability in the Replicative Polymerase Active Site.,Zahn KE, Averill A, Wallace SS, Doublie S Biochemistry. 2011 Nov 3. PMID:22026756<ref>PMID:22026756</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 3tab" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bpr69]]~~		[[Category: Escherichia phage RB69]]
	~~[[Category: DNA-directed DNA polymerase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Zahn~~, K E]]~~		[[Category: Zahn KE]]
	~~[[Category: Transferase-dna complex~~]]

OCA at 16:49, 6 July 2022

2022-07-06T16:49:37Z

← Older revision		Revision as of 16:49, 6 July 2022
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	<StructureSection load='3tab' size='340' side='right'caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3tab' size='340' side='right'caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TAB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OC:2-DEOXY-5-HYDROXYCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5OC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OC:2-DEOXY-5-HYDROXYCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5OC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tae\|3tae]], [[3taf\|3taf]], [[3tag\|3tag]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tae\|3tae]], [[3taf\|3taf]], [[3tag\|3tag]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [~~http~~://pdbe.org/3tab PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tab PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tab 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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [https://pdbe.org/3tab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [https://www.ebi.ac.uk/pdbsum/3tab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.		[[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 3tab" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3tab" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:40, 17 July 2019

2019-07-17T11:40:27Z

← Older revision		Revision as of 11:40, 17 July 2019
Line 1:		Line 1:

	==5-hydroxycytosine paired with dGMP in RB69 gp43==		==5-hydroxycytosine paired with dGMP in RB69 gp43==
	<StructureSection load='3tab' size='340' side='right' caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3tab' size='340' side='right'caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAB FirstGlance]. <br>
Line 24:		Line 24:

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bpr69]]		[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
			[[Category: Large Structures]]
	[[Category: Zahn, K E]]		[[Category: Zahn, K E]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 01:20, 5 August 2016

2016-08-05T01:20:26Z

← Older revision		Revision as of 01:20, 5 August 2016
Line 1:		Line 1:

	==5-hydroxycytosine paired with dGMP in RB69 gp43==		==5-hydroxycytosine paired with dGMP in RB69 gp43==
	<StructureSection load='3tab' size='340' side='right' caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3tab' size='340' side='right' caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_rb69 Enterobacteria phage rb69~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OC:2-DEOXY-5-HYDROXYCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5OC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OC:2-DEOXY-5-HYDROXYCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5OC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tae\|3tae]], [[3taf\|3taf]], [[3tag\|3tag]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tae\|3tae]], [[3taf\|3taf]], [[3tag\|3tag]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 ~~Enterobacteria phage RB69~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [http://www.ebi.ac.uk/pdbsum/3tab 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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [http://pdbe.org/3tab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [http://www.ebi.ac.uk/pdbsum/3tab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 3tab" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	~~[[Category: Enterobacteria phage rb69]]~~
	[[Category: Zahn, K E]]		[[Category: Zahn, K E]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 21:33, 24 December 2014

2014-12-24T21:33:32Z

← Older revision		Revision as of 21:33, 24 December 2014
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	<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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [http://www.ebi.ac.uk/pdbsum/3tab 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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [http://www.ebi.ac.uk/pdbsum/3tab PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:28, 9 December 2014

2014-12-09T12:28:01Z

← Older revision		Revision as of 12:28, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~3tab~~.~~png~~\|~~left~~\|~~200px~~]]		==5-hydroxycytosine paired with dGMP in RB69 gp43==
			<StructureSection load='3tab' size='340' side='right' caption='[[3tab]], [[Resolution\|resolution]] 2.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3tab]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAB FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OC:2-DEOXY-5-HYDROXYCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5OC</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tae\|3tae]], [[3taf\|3taf]], [[3tag\|3tag]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69])</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=3tab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tab OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tab RCSB], [http://www.ebi.ac.uk/pdbsum/3tab PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			5-Hydroxycytosine (5-OHC) is a stable oxidation product of cytosine associated with an increased frequency of C --> T transition mutations. When this lesion escapes recognition by the base excision repair pathway and persists to serve as a templating base during DNA synthesis, replicative DNA polymerases often misincorporate dAMP at the primer terminus, which can lead to fixation of mutations and subsequent disease. To characterize the dynamics of DNA synthesis opposite 5-OHC, we initiated a comparison of unmodified dCMP to 5-OHC, 5-fluorocytosine (5-FC), and 5-methylcytosine (5-MEC) in which these bases act as templates in the active site of RB69 gp43, a high-fidelity DNA polymerase sharing homology with human replicative DNA polymerases. This study presents the first crystal structure of any DNA polymerase binding this physiologically important premutagenic DNA lesion, showing that while dGMP is stabilized by 5-OHC through normal Watson-Crick base pairing, incorporation of dAMP leads to unstacking and instability in the template. Furthermore, the electronegativity of the C5 substituent appears to be important in the miscoding potential of these cytosine-like templates. While dAMP is incorporated opposite 5-OHC approximately 5 times more efficiently than opposite unmodified dCMP, an elevated level of incorporation is also observed opposite 5-FC but not 5-MEC. Taken together, these data imply that the nonuniform templating by 5-OHC is due to weakened stacking capabilities, which allows dAMP incorporation to proceed in a manner similar to that observed opposite abasic sites.

	~~{{STRUCTURE_3tab\| PDB=3tab \| SCENE= }}~~		The Miscoding Potential of 5-Hydroxycytosine Arises Due to Template Instability in the Replicative Polymerase Active Site.,Zahn KE, Averill A, Wallace SS, Doublie S Biochemistry. 2011 Nov 3. PMID:22026756<ref>PMID:22026756</ref>

	~~===5-hydroxycytosine paired with dGMP in RB69 gp43===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22026756}}~~

	~~==About this Structure==~~
	~~[[3tab]] is~~ a ~~12 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=3TAB OCA].~~

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:022026756<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]
	[[Category: Zahn, K E.]]		[[Category: Zahn, K E]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 09:20, 20 October 2012

2012-10-20T09:20:59Z

← Older revision		Revision as of 09:20, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[3tab]] is a 12 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA].		[[3tab]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA].

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

OCA at 22:34, 25 July 2012

2012-07-25T22:34:01Z

← Older revision		Revision as of 22:34, 25 July 2012
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	[[Image:3tab.png\|left\|200px]]		[[Image:3tab.png\|left\|200px]]

	~~<!--~~
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	~~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_3tab\| PDB=3tab \| SCENE= }}		{{STRUCTURE_3tab\| PDB=3tab \| SCENE= }}

	===5-hydroxycytosine paired with dGMP in RB69 gp43===		===5-hydroxycytosine paired with dGMP in RB69 gp43===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22026756}}, adds the Publication Abstract to the page~~
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	==See Also==		==See Also==
	*[[DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==

OCA at 05:37, 11 January 2012

2012-01-11T05:37:01Z

← Older revision		Revision as of 05:37, 11 January 2012
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	[[Image:3tab.~~jpg~~\|left\|200px]]		[[Image:3tab.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
	[[3tab]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA].		[[3tab]] is a 12 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAB OCA].

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

	==Reference==		==Reference==

OCA at 11:37, 9 November 2011

2011-11-09T11:37:39Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:3tab.jpg|left|200px]]
-The entry 3tab is ON HOLD  until Paper Publication
+<!--
-Authors: Zahn, K.E.
+===5-hydroxycytosine paired with dGMP in RB69 gp43===
-Description: 5-hydroxycytosine paired with dGMP in RB69 gp43