3pvx - Revision history

OCA at 10:43, 21 February 2024

OCA — Wed, 21 Feb 2024 10:43:51 GMT

←Older revision		Revision as of 10:43, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3pvx' size='340' side='right'caption='[[3pvx]], [[Resolution\|resolution]] 3.03Å' scene=''>		<StructureSection load='3pvx' size='340' side='right'caption='[[3pvx]], [[Resolution\|resolution]] 3.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pvx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_35091 Atcc 35091~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pvx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PVX FirstGlance]. <br>
-	</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>~~</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]] 3.03Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PVX~~:'>~~PVX~~</scene><~~/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=PVX:N-(2-amino-5-{formyl[(6aS,8R,9R,9aR)-9-hydroxy-4-methoxy-1,11-dioxo-1,6a,8,9,9a,11-hexahydrocyclopenta[c]furo[3,2 4,5]furo[2,3-h]chromen-8-yl]amino}-6-oxo-1,6-dihydropyrimidin-4-yl)-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine'>PVX</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;'>~~[~~[3pw0\|3pw0]]~~, ~~[[3pw2\|3pw2]]~~, ~~[[3pw4\|3pw4]]~~, ~~[[3pw5\|3pw5]]~~, [~~[3pw7\|3pw7~~]~~]</div></td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>~~[~~[Gene\|Gene:]]</b></td><td class="sblockDat">dbh~~, ~~dpo4~~, ~~SSO2448 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=2287 ATCC 35091~~]~~)</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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [https://pdbe.org/3pvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [https://www.ebi.ac.uk/pdbsum/3pvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pvx 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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [https://pdbe.org/3pvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [https://www.ebi.ac.uk/pdbsum/3pvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pvx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~DPO4_SULSO DPO4_SULSO]~~] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis~~.[HAMAP-Rule:MF_01113]~~	+	[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Aflatoxin B(1) (AFB(1)) is oxidized to an epoxide in vivo, which forms an N7-dG DNA adduct (AFB(1)-N7-dG). The AFB(1)-N7-dG can rearrange to a formamidopyrimidine (AFB(1)-FAPY) derivative. Both AFB(1)-N7-dG and the beta-anomer of the AFB(1)-FAPY adduct yield G-->T transversions in Escherichia coli, but the latter is more mutagenic. We show that the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) bypasses AFB(1)-N7-dG in an error-free manner but conducts error-prone replication past the AFB(1)-FAPY adduct, including misinsertion of dATP, consistent with the G-->T mutations observed in E. coli. Three ternary (Dpo4-DNA-dNTP) structures with AFB(1)-N7-dG adducted template:primers have been solved. These demonstrate insertion of dCTP opposite the AFB(1)-N7-dG adduct, and correct vs incorrect insertion of dATP vs dTTP opposite the 5'-template neighbor dT from a primed AFB(1)-N7-dG:dC pair. The insertion of dTTP reveals hydrogen bonding between the template N3 imino proton and the O(2) oxygen of dTTP, and between the template T O(4) oxygen and the N3 imino proton of dTTP, perhaps explaining why this polymerase does not efficiently catalyze phosphodiester bond formation from this mispair. The AFB(1)-N7-dG maintains the 5'-intercalation of the AFB(1) moiety observed in DNA. The bond between N7-dG and C8 of the AFB(1) moiety remains in plane with the alkylated guanine, creating a 16 degrees inclination of the AFB(1) moiety with respect to the guanine. A binary (Dpo4-DNA) structure with an AFB(1)-FAPY adducted template:primer also maintains 5'-intercalation of the AFB(1) moiety. The beta-deoxyribose anomer is observed. Rotation about the FAPY C5-N(5) bond orients the bond between N(5) and C8 of the AFB(1) moiety out of plane in the 5'-direction, with respect to the FAPY base. The formamide group extends in the 3'-direction. This improves stacking of the AFB(1) moiety above the 5'-face of the FAPY base, as compared to the AFB(1)-N7-dG adduct. Ternary structures with AFB(1)-beta-FAPY adducted template:primers show correct vs incorrect insertion of dATP vs dTTP opposite the 5'-template neighbor dT from a primed AFB(1)-beta-FAPY:dC pair. For dATP, the oxygen atom of the FAPY formamide group participates in a water-mediated hydrogen bond with Arg332. The insertion of dTTP yields a structure similar to that observed for the AFB(1)-N7-dG adduct. The differential accommodation of these AFB(1) adducts within the active site may, in part, modulate lesion bypass.	+

-	~~Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV.,Banerjee S, Brown KL, Egli M, Stone MP J Am Chem Soc. 2011 Jul 26. PMID:21790157<ref>PMID:21790157</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 3pvx" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 35091]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Banerjee, S~~]]	+	[[Category: Saccharolobus solfataricus]]
-	[[Category: ~~Dna adduct~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Dna polymerase]]~~	+	[[Category: Banerjee S]]
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 08:58, 25 May 2022

OCA — Wed, 25 May 2022 08:58:23 GMT

←Older revision		Revision as of 08:58, 25 May 2022
Line 1:		Line 1:

	==Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV==		==Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV==
-	<StructureSection load='3pvx' size='340' side='right' caption='[[3pvx]], [[Resolution\|resolution]] 3.03Å' scene=''>	+	<StructureSection load='3pvx' size='340' side='right'caption='[[3pvx]], [[Resolution\|resolution]] 3.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pvx]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pvx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PVX 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></td></tr>	+	</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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PVX:'>PVX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PVX:'>PVX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pw0\|3pw0]], [[3pw2\|3pw2]], [[3pw4\|3pw4]], [[3pw5\|3pw5]], [[3pw7\|3pw7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pw0\|3pw0]], [[3pw2\|3pw2]], [[3pw4\|3pw4]], [[3pw5\|3pw5]], [[3pw7\|3pw7]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [~~http~~://pdbe.org/3pvx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pvx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pvx 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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [https://pdbe.org/3pvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [https://www.ebi.ac.uk/pdbsum/3pvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pvx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPO4_SULSO DPO4_SULSO]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]	+	[[https://www.uniprot.org/uniprot/DPO4_SULSO DPO4_SULSO]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]
	<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 3pvx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pvx" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 28:
	[[Category: Atcc 35091]]		[[Category: Atcc 35091]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Banerjee, S]]		[[Category: Banerjee, S]]
	[[Category: Dna adduct]]		[[Category: Dna adduct]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 20:37, 4 August 2016

OCA — Thu, 04 Aug 2016 20:37:11 GMT

←Older revision		Revision as of 20:37, 4 August 2016
Line 1:		Line 1:
		+
	==Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV==		==Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV==
	<StructureSection load='3pvx' size='340' side='right' caption='[[3pvx]], [[Resolution\|resolution]] 3.03Å' scene=''>		<StructureSection load='3pvx' size='340' side='right' caption='[[3pvx]], [[Resolution\|resolution]] 3.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pvx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus Sulfolobus solfataricus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pvx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PVX 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PVX:'>PVX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PVX:'>PVX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pw0\|3pw0]], [[3pw2\|3pw2]], [[3pw4\|3pw4]], [[3pw5\|3pw5]], [[3pw7\|3pw7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pw0\|3pw0]], [[3pw2\|3pw2]], [[3pw4\|3pw4]], [[3pw5\|3pw5]], [[3pw7\|3pw7]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ~~Sulfolobus solfataricus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [http://www.ebi.ac.uk/pdbsum/3pvx 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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [http://pdbe.org/3pvx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [http://www.ebi.ac.uk/pdbsum/3pvx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pvx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~DPO42_SULSO DPO42_SULSO~~]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]	+	[[http://www.uniprot.org/uniprot/DPO4_SULSO DPO4_SULSO]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:
	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 3pvx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 35091]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Sulfolobus solfataricus]]
	[[Category: Banerjee, S]]		[[Category: Banerjee, S]]
	[[Category: Dna adduct]]		[[Category: Dna adduct]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 12:56, 25 December 2014

OCA — Thu, 25 Dec 2014 12:56:55 GMT

←Older revision		Revision as of 12:56, 25 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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [http://www.ebi.ac.uk/pdbsum/3pvx 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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [http://www.ebi.ac.uk/pdbsum/3pvx PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO42_SULSO DPO42_SULSO]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 13:13, 9 December 2014

OCA — Tue, 09 Dec 2014 13:13:41 GMT

←Older revision		Revision as of 13:13, 9 December 2014
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-	[[~~Image:~~3pvx.~~png~~\|~~left~~\|~~200px~~]]	+	==Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV==
		+	<StructureSection load='3pvx' size='340' side='right' caption='[[3pvx]], [[Resolution\|resolution]] 3.03Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3pvx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PVX 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></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PVX:'>PVX</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pw0\|3pw0]], [[3pw2\|3pw2]], [[3pw4\|3pw4]], [[3pw5\|3pw5]], [[3pw7\|3pw7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</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=3pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pvx RCSB], [http://www.ebi.ac.uk/pdbsum/3pvx PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aflatoxin B(1) (AFB(1)) is oxidized to an epoxide in vivo, which forms an N7-dG DNA adduct (AFB(1)-N7-dG). The AFB(1)-N7-dG can rearrange to a formamidopyrimidine (AFB(1)-FAPY) derivative. Both AFB(1)-N7-dG and the beta-anomer of the AFB(1)-FAPY adduct yield G-->T transversions in Escherichia coli, but the latter is more mutagenic. We show that the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) bypasses AFB(1)-N7-dG in an error-free manner but conducts error-prone replication past the AFB(1)-FAPY adduct, including misinsertion of dATP, consistent with the G-->T mutations observed in E. coli. Three ternary (Dpo4-DNA-dNTP) structures with AFB(1)-N7-dG adducted template:primers have been solved. These demonstrate insertion of dCTP opposite the AFB(1)-N7-dG adduct, and correct vs incorrect insertion of dATP vs dTTP opposite the 5'-template neighbor dT from a primed AFB(1)-N7-dG:dC pair. The insertion of dTTP reveals hydrogen bonding between the template N3 imino proton and the O(2) oxygen of dTTP, and between the template T O(4) oxygen and the N3 imino proton of dTTP, perhaps explaining why this polymerase does not efficiently catalyze phosphodiester bond formation from this mispair. The AFB(1)-N7-dG maintains the 5'-intercalation of the AFB(1) moiety observed in DNA. The bond between N7-dG and C8 of the AFB(1) moiety remains in plane with the alkylated guanine, creating a 16 degrees inclination of the AFB(1) moiety with respect to the guanine. A binary (Dpo4-DNA) structure with an AFB(1)-FAPY adducted template:primer also maintains 5'-intercalation of the AFB(1) moiety. The beta-deoxyribose anomer is observed. Rotation about the FAPY C5-N(5) bond orients the bond between N(5) and C8 of the AFB(1) moiety out of plane in the 5'-direction, with respect to the FAPY base. The formamide group extends in the 3'-direction. This improves stacking of the AFB(1) moiety above the 5'-face of the FAPY base, as compared to the AFB(1)-N7-dG adduct. Ternary structures with AFB(1)-beta-FAPY adducted template:primers show correct vs incorrect insertion of dATP vs dTTP opposite the 5'-template neighbor dT from a primed AFB(1)-beta-FAPY:dC pair. For dATP, the oxygen atom of the FAPY formamide group participates in a water-mediated hydrogen bond with Arg332. The insertion of dTTP yields a structure similar to that observed for the AFB(1)-N7-dG adduct. The differential accommodation of these AFB(1) adducts within the active site may, in part, modulate lesion bypass.

-	~~{{STRUCTURE_3pvx\| PDB=3pvx \| SCENE= }}~~	+	Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV.,Banerjee S, Brown KL, Egli M, Stone MP J Am Chem Soc. 2011 Jul 26. PMID:21790157<ref>PMID:21790157</ref>

-	~~===Binary complex~~ of ~~Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21790157}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3pvx]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021790157<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
-	[[Category: Banerjee, S.]]	+	[[Category: Banerjee, S]]
	[[Category: Dna adduct]]		[[Category: Dna adduct]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 16:56, 20 October 2012

OCA — Sat, 20 Oct 2012 16:56:23 GMT

←Older revision		Revision as of 16:56, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3pvx]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA].	+	[[3pvx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA].

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

OCA at 23:18, 26 July 2012

OCA — Thu, 26 Jul 2012 23:18:18 GMT

←Older revision		Revision as of 23:18, 26 July 2012
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	[[Image:3pvx.png\|left\|200px]]		[[Image:3pvx.png\|left\|200px]]

-	<!--
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-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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	{{STRUCTURE_3pvx\| PDB=3pvx \| SCENE= }}		{{STRUCTURE_3pvx\| PDB=3pvx \| SCENE= }}

	===Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV===		===Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21790157}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21790157 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_21790157}}		{{ABSTRACT_PUBMED_21790157}}

	==About this Structure==		==About this Structure==
-	[[3pvx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA].	+	[[3pvx]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==

OCA at 04:59, 21 September 2011

OCA — Wed, 21 Sep 2011 04:59:26 GMT

←Older revision		Revision as of 04:59, 21 September 2011
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-	[[Image:3pvx.~~jpg~~\|left\|200px]]	+	[[Image:3pvx.png\|left\|200px]]

	<!--		<!--

OCA at 05:57, 10 August 2011

OCA — Wed, 10 Aug 2011 05:57:22 GMT

←Older revision		Revision as of 05:57, 10 August 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3pvx.jpg\|left\|200px]]

-	The ~~entry 3pvx~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3pvx", 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_3pvx\| PDB=3pvx \| SCENE= }}

-	~~Authors: Banerjee, S.~~	+	===Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV===

-	~~Description~~: ~~Bypass of Aflatoxin B1 Adducts by~~ the Sulfolobus solfataricus DNA ~~Polymerase IV~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21790157}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21790157 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21790157}}
		+
		+	==About this Structure==
		+	[[3pvx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVX OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021790157</ref><references group="xtra"/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Sulfolobus solfataricus]]
		+	[[Category: Banerjee, S.]]
		+	[[Category: Dna adduct]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Transferase-dna complex]]

OCA at 06:36, 2 March 2011

OCA — Wed, 02 Mar 2011 06:36:24 GMT

←Older revision		Revision as of 06:36, 2 March 2011
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3pvx is ON HOLD	+	The entry 3pvx is ON HOLD until Paper Publication

	Authors: Banerjee, S.		Authors: Banerjee, S.

	Description: Bypass of Aflatoxin B1 Adducts by the Sulfolobus solfataricus DNA Polymerase IV		Description: Bypass of Aflatoxin B1 Adducts by the Sulfolobus solfataricus DNA Polymerase IV