4rzr - Revision history

OCA at 12:57, 1 March 2024

OCA — Fri, 01 Mar 2024 12:57:25 GMT

←Older revision		Revision as of 12:57, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rzr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2] 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=4RZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rzr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2] 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=4RZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2JV:N-(8-AMINOPYREN-1-YL)-2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)GUANOSINE'>2JV</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2JV:N-(8-AMINOPYREN-1-YL)-2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)GUANOSINE'>2JV</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=4rzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzr OCA], [https://pdbe.org/4rzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzr RCSB], [https://www.ebi.ac.uk/pdbsum/4rzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzr 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=4rzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzr OCA], [https://pdbe.org/4rzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzr RCSB], [https://www.ebi.ac.uk/pdbsum/4rzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[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.		[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 ==
-	1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo. Our running start assays confirmed that a site-specifically placed 8-(deoxyguanosin-N(2)-yl)-1-aminopyrene (dG(1,8)), one of the DNA adducts derived from 1-NP, can be bypassed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), although this representative Y-family enzyme was paused strongly by the lesion. Pre-steady-state kinetic assays were employed to determine the low nucleotide incorporation fidelity and establish a minimal kinetic mechanism for the dG(1,8) bypass by Dpo4. To reveal a structural basis for dCTP incorporation opposite dG(1,8), we solved the crystal structures of the complexes of Dpo4 and DNA containing a templating dG(1,8) lesion in the absence or presence of dCTP. The Dpo4.DNA-dG(1,8) binary structure shows that the aminopyrene moiety of the lesion stacks against the primer/template junction pair, while its dG moiety projected into the cleft between the Finger and Little Finger domains of Dpo4. In the Dpo4.DNA-dG(1,8).dCTP ternary structure, the aminopyrene moiety of the dG(1,8) lesion, is sandwiched between the nascent and junction base pairs, while its base is present in the major groove. Moreover, dCTP forms a Watson-Crick base pair with dG, two nucleotides upstream from the dG(1,8) site, creating a complex for "-2" frameshift mutation. Mechanistically, these crystal structures provide additional insight into the aforementioned minimal kinetic mechanism.
-
-	Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase.,Vyas R, Efthimiopoulos G, Tokarsky EJ, Malik CK, Basu AK, Suo Z J Am Chem Soc. 2015 Sep 23;137(37):12131-42. doi: 10.1021/jacs.5b08027. Epub 2015, Sep 11. PMID:26327169<ref>PMID:26327169</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rzr" style="background-color:#fffaf0;"></div>

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

OCA at 10:36, 15 March 2023

OCA — Wed, 15 Mar 2023 10:36:33 GMT

←Older revision		Revision as of 10:36, 15 March 2023
Line 1:		Line 1:

	==Bypass of a bulky adduct dG1,8 by DPO4==		==Bypass of a bulky adduct dG1,8 by DPO4==
-	<StructureSection load='4rzr' size='340' side='right' caption='[[4rzr]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4rzr' size='340' side='right'caption='[[4rzr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rzr]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sulso Sulso~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RZR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rzr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2] 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=4RZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZR 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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2JV:N-(8-AMINOPYREN-1-YL)-2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)GUANOSINE'>2JV</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JV:N-(8-AMINOPYREN-1-YL)-2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)GUANOSINE'>2JV</scene></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=4rzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzr OCA], [https://pdbe.org/4rzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzr RCSB], [https://www.ebi.ac.uk/pdbsum/4rzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzr ProSAT]</span></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=273057 SULSO])</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=4rzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzr OCA], [~~http~~://pdbe.org/4rzr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rzr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rzr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzr 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_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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4rzr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4rzr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Sulso~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: ~~Suo, Z~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Vyas, R~~]]	+	[[Category: Suo Z]]
-	[[Category: ~~Dbh]]~~	+	[[Category: Vyas R]]
-	~~[[Category: Dpo4]]~~	+
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 16:57, 16 November 2017

OCA — Thu, 16 Nov 2017 16:57:07 GMT

←Older revision		Revision as of 16:57, 16 November 2017
Line 1:		Line 1:
		+
	==Bypass of a bulky adduct dG1,8 by DPO4==		==Bypass of a bulky adduct dG1,8 by DPO4==
	<StructureSection load='4rzr' size='340' side='right' caption='[[4rzr]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4rzr' size='340' side='right' caption='[[4rzr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rzr]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rzr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZR 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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JV:N-(8-AMINOPYREN-1-YL)-2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)GUANOSINE'>2JV</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JV:N-(8-AMINOPYREN-1-YL)-2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)GUANOSINE'>2JV</scene></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=273057 SULSO])</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=4rzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzr OCA], [http://pdbe.org/4rzr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzr RCSB], [http://www.ebi.ac.uk/pdbsum/4rzr 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=4rzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzr OCA], [http://pdbe.org/4rzr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzr RCSB], [http://www.ebi.ac.uk/pdbsum/4rzr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Sulso]]
	[[Category: Suo, Z]]		[[Category: Suo, Z]]
	[[Category: Vyas, R]]		[[Category: Vyas, R]]

OCA at 07:34, 7 October 2015

OCA — Wed, 07 Oct 2015 07:34:20 GMT

←Older revision		Revision as of 07:34, 7 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Bypass of a bulky adduct dG1,8 by DPO4==
		+	<StructureSection load='4rzr' size='340' side='right' caption='[[4rzr]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rzr]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZR 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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JV:N-(8-AMINOPYREN-1-YL)-2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)GUANOSINE'>2JV</scene></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=4rzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzr OCA], [http://pdbe.org/4rzr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzr RCSB], [http://www.ebi.ac.uk/pdbsum/4rzr PDBsum]</span></td></tr>
		+	</table>
		+	== 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]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo. Our running start assays confirmed that a site-specifically placed 8-(deoxyguanosin-N(2)-yl)-1-aminopyrene (dG(1,8)), one of the DNA adducts derived from 1-NP, can be bypassed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), although this representative Y-family enzyme was paused strongly by the lesion. Pre-steady-state kinetic assays were employed to determine the low nucleotide incorporation fidelity and establish a minimal kinetic mechanism for the dG(1,8) bypass by Dpo4. To reveal a structural basis for dCTP incorporation opposite dG(1,8), we solved the crystal structures of the complexes of Dpo4 and DNA containing a templating dG(1,8) lesion in the absence or presence of dCTP. The Dpo4.DNA-dG(1,8) binary structure shows that the aminopyrene moiety of the lesion stacks against the primer/template junction pair, while its dG moiety projected into the cleft between the Finger and Little Finger domains of Dpo4. In the Dpo4.DNA-dG(1,8).dCTP ternary structure, the aminopyrene moiety of the dG(1,8) lesion, is sandwiched between the nascent and junction base pairs, while its base is present in the major groove. Moreover, dCTP forms a Watson-Crick base pair with dG, two nucleotides upstream from the dG(1,8) site, creating a complex for "-2" frameshift mutation. Mechanistically, these crystal structures provide additional insight into the aforementioned minimal kinetic mechanism.

-	~~The entry 4rzr is ON HOLD until Paper Publication~~	+	Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase.,Vyas R, Efthimiopoulos G, Tokarsky EJ, Malik CK, Basu AK, Suo Z J Am Chem Soc. 2015 Sep 23;137(37):12131-42. doi: 10.1021/jacs.5b08027. Epub 2015, Sep 11. PMID:26327169<ref>PMID:26327169</ref>

-	~~Authors: Vyas~~, R.~~, Suo, Z~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Bypass of a bulky adduct dG1,8 by DPO4~~	+	<div class="pdbe-citations 4rzr" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
	[[Category: Suo, Z]]		[[Category: Suo, Z]]
	[[Category: Vyas, R]]		[[Category: Vyas, R]]
		+	[[Category: Dbh]]
		+	[[Category: Dpo4]]
		+	[[Category: Polymerase]]
		+	[[Category: Transferase-dna complex]]

OCA at 14:07, 21 January 2015

OCA — Wed, 21 Jan 2015 14:07:22 GMT

←Older revision		Revision as of 14:07, 21 January 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rzr is ON HOLD	+	The entry 4rzr is ON HOLD until Paper Publication

	Authors: Vyas, R., Suo, Z.		Authors: Vyas, R., Suo, Z.

OCA at 10:56, 14 January 2015

OCA — Wed, 14 Jan 2015 10:56:45 GMT

←Older revision		Revision as of 10:56, 14 January 2015
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	Authors: Vyas, R., Suo, Z.		Authors: Vyas, R., Suo, Z.

-	Description: ~~BYPASS OF~~ a bulky adduct, dG1,8 BY DPO4	+	Description: Bypass of a bulky adduct dG1,8 by DPO4
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Suo, Z]]		[[Category: Suo, Z]]
	[[Category: Vyas, R]]		[[Category: Vyas, R]]

OCA: Protected "4rzr" [edit=sysop:move=sysop]

OCA — Wed, 31 Dec 2014 12:18:13 GMT

Protected "4rzr" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:18, 31 December 2014

OCA: New page: '''Unreleased structure''' The entry 4rzr is ON HOLD Authors: Vyas, R., Suo, Z. Description: BYPASS OF a bulky adduct, dG1,8 BY DPO4 Category: Unreleased Structures [[Category: Suo...

OCA — Wed, 31 Dec 2014 12:18:12 GMT

New page: '''Unreleased structure''' The entry 4rzr is ON HOLD Authors: Vyas, R., Suo, Z. Description: BYPASS OF a bulky adduct, dG1,8 BY DPO4 Category: Unreleased Structures [[Category: Suo...

New page

'''Unreleased structure'''

The entry 4rzr is ON HOLD

Authors: Vyas, R., Suo, Z.

Description: BYPASS OF a bulky adduct, dG1,8 BY DPO4
[[Category: Unreleased Structures]]
[[Category: Suo, Z]]
[[Category: Vyas, R]]