5wm8 - Revision history

OCA at 14:17, 4 October 2023

OCA — Wed, 04 Oct 2023 14:17:08 GMT

←Older revision		Revision as of 14:17, 4 October 2023
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	<StructureSection load='5wm8' size='340' side='right'caption='[[5wm8]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='5wm8' size='340' side='right'caption='[[5wm8]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wm8]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WM8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wm8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] 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=5WM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WM8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.92Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wm1\|5wm1]]</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=5wm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wm8 OCA], [https://pdbe.org/5wm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wm8 RCSB], [https://www.ebi.ac.uk/pdbsum/5wm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wm8 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REV1, YOR346W, O6339 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5wm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wm8 OCA], [~~http~~://pdbe.org/5wm8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wm8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wm8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wm8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST]] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>	+	[https://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>
	<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 5wm8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wm8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Aggarwal, A K~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Geacintov, N E~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Kolbanovsky, A~~]]	+	[[Category: Aggarwal AK]]
-	[[Category: ~~Landes, H~~]]	+	[[Category: Geacintov NE]]
-	[[Category: ~~Rechkoblit, O~~]]	+	[[Category: Kolbanovsky A]]
-	[[Category: ~~Dna binding protein~~]]	+	[[Category: Landes H]]
-	[[Category: ~~Transferase-dna complex~~]]	+	[[Category: Rechkoblit O]]

OCA at 09:11, 18 December 2019

OCA — Wed, 18 Dec 2019 09:11:53 GMT

←Older revision		Revision as of 09:11, 18 December 2019
Line 1:		Line 1:

	==Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex==		==Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex==
-	<StructureSection load='5wm8' size='340' side='right' caption='[[5wm8]], [[Resolution\|resolution]] 1.92Å' scene=''>	+	<StructureSection load='5wm8' size='340' side='right'caption='[[5wm8]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5wm8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WM8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5wm8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WM8 FirstGlance]. <br>
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Aggarwal, A K]]		[[Category: Aggarwal, A K]]
	[[Category: Geacintov, N E]]		[[Category: Geacintov, N E]]

OCA at 06:12, 1 November 2017

OCA — Wed, 01 Nov 2017 06:12:51 GMT

←Older revision		Revision as of 06:12, 1 November 2017
Line 3:		Line 3:
	<StructureSection load='5wm8' size='340' side='right' caption='[[5wm8]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='5wm8' size='340' side='right' caption='[[5wm8]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wm8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wm8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WM8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wm1\|5wm1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wm1\|5wm1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REV1, YOR346W, O6339 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5wm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wm8 OCA], [http://pdbe.org/5wm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wm8 RCSB], [http://www.ebi.ac.uk/pdbsum/5wm8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wm8 ProSAT]</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=5wm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wm8 OCA], [http://pdbe.org/5wm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wm8 RCSB], [http://www.ebi.ac.uk/pdbsum/5wm8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wm8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST]] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>		[[http://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST]] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke which, after metabolic activation, can react with the exocyclic N 2 amino group of guanine to generate four stereoisomeric BP-N 2-dG adducts. Rev1 is unique among translesion synthesis DNA polymerases in employing a protein-template-directed mechanism of DNA synthesis opposite undamaged and damaged guanine. Here we report high-resolution structures of yeast Rev1 with three BP-N 2-dG adducts, namely the 10S (+)-trans-BP-N 2-dG, 10R (+)-cis-BP-N 2-dG, and 10S ( - )-cis-BP-N 2-dG. Surprisingly, in all three structures, the bulky and hydrophobic BP pyrenyl residue is entirely solvent-exposed in the major groove of the DNA. This is very different from the adduct alignments hitherto observed in free or protein-bound DNA. All complexes are well poised for dCTP insertion. Our structures provide a view of cis-BP-N 2-dG adducts in a DNA polymerase active site, and offer a basis for understanding error-free replication of the BP-derived stereoisomeric guanine adducts.Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke that upon metabolic activation reacts with guanine. Here, the authors present the structures of the translesion DNA synthesis polymerase Rev1 in complex with three of the four possible stereoisomeric BP-N 2 -dG adducts, which gives insights how Rev1 achieves error-free replication.
		+
		+	Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase.,Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE, Aggarwal AK Nat Commun. 2017 Oct 17;8(1):965. doi: 10.1038/s41467-017-01013-5. PMID:29042535<ref>PMID:29042535</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5wm8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Aggarwal, A K]]		[[Category: Aggarwal, A K]]
	[[Category: Geacintov, N E]]		[[Category: Geacintov, N E]]

OCA at 07:18, 25 October 2017

OCA — Wed, 25 Oct 2017 07:18:54 GMT

←Older revision		Revision as of 07:18, 25 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wm8 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex==
-		+	<StructureSection load='5wm8' size='340' side='right' caption='[[5wm8]], [[Resolution\|resolution]] 1.92Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5wm8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WM8 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wm1\|5wm1]]</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=5wm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wm8 OCA], [http://pdbe.org/5wm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wm8 RCSB], [http://www.ebi.ac.uk/pdbsum/5wm8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wm8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST]] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aggarwal, A K]]
		+	[[Category: Geacintov, N E]]
		+	[[Category: Kolbanovsky, A]]
		+	[[Category: Landes, H]]
		+	[[Category: Rechkoblit, O]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Transferase-dna complex]]

OCA: Protected "5wm8" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:58:40 GMT

Protected "5wm8" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:58, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5wm8 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 14:58:39 GMT

New page: '''Unreleased structure''' The entry 5wm8 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5wm8 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]