3raq - Revision history

OCA at 10:37, 4 August 2016

2016-08-04T10:37:05Z

← Older revision		Revision as of 10:37, 4 August 2016
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	==Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion==		==Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion==
	<StructureSection load='3raq' size='340' side='right' caption='[[3raq]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3raq' size='340' side='right' caption='[[3raq]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3raq]] is a 6 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=3RAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RAQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3raq]] is a 6 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=3RAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RAQ 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG1:2-DEOXY-1-METHYLGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>MG1</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG1:2-DEOXY-1-METHYLGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>MG1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gik\|3gik]], [[2asd\|2asd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gik\|3gik]], [[2asd\|2asd]]</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=3raq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3raq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3raq RCSB], [http://www.ebi.ac.uk/pdbsum/3raq 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=3raq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3raq OCA], [http://pdbe.org/3raq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3raq RCSB], [http://www.ebi.ac.uk/pdbsum/3raq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3raq 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 3raq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Atcc 35091]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	~~[[Category: Sulfolobus solfataricus]]~~
	[[Category: Patel, D J]]		[[Category: Patel, D J]]
	[[Category: Rechkoblit, O]]		[[Category: Rechkoblit, O]]

OCA at 08:25, 25 December 2014

2014-12-25T08:25:14Z

← Older revision		Revision as of 08:25, 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=3raq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3raq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3raq RCSB], [http://www.ebi.ac.uk/pdbsum/3raq 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=3raq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3raq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3raq RCSB], [http://www.ebi.ac.uk/pdbsum/3raq PDBsum]</span></td></tr>
	</table>		</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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:56, 19 December 2014

2014-12-19T10:56:57Z

← Older revision		Revision as of 10:56, 19 December 2014
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	~~{{STRUCTURE_3raq\| PDB=3raq \| SCENE= }}~~		==Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion==
	===Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion===		<StructureSection load='3raq' size='340' side='right' caption='[[3raq]], [[Resolution\|resolution]] 2.25Å' scene=''>
	~~{{ABSTRACT_PUBMED_21645853}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3raq]] is a 6 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=3RAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RAQ 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG1:2-DEOXY-1-METHYLGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>MG1</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gik\|3gik]], [[2asd\|2asd]]</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=3raq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3raq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3raq RCSB], [http://www.ebi.ac.uk/pdbsum/3raq PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			DNA is susceptible to alkylation damage by a number of environmental agents that modify the Watson-Crick edge of the bases. Such lesions, if not repaired, may be bypassed by Y-family DNA polymerases. The bypass polymerase Dpo4 is strongly inhibited by 1-methylguanine (m1G) and 3-methylcytosine (m3C), with nucleotide incorporation opposite these lesions being predominantly mutagenic. Further, extension after insertion of both correct and incorrect bases, introduces additional base substitution and deletion errors. Crystal structures of the Dpo4 ternary extension complexes with correct and mismatched 3'-terminal primer bases opposite the lesions reveal that both m1G and m3C remain positioned within the DNA template/primer helix. However, both correct and incorrect pairing partners exhibit pronounced primer terminal nucleotide distortion, being primarily evicted from the DNA helix when opposite m1G or misaligned when pairing with m3C. Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases.

	~~==Function==~~		Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions.,Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ Structure. 2011 Jun 8;19(6):821-32. doi: 10.1016/j.str.2011.03.020. PMID:21645853<ref>PMID:21645853</ref>
	~~[[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]~~

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[3raq]] is~~ a ~~6 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=3RAQ OCA].~~		</div>

	==~~Reference~~==		==See Also==
	~~<ref group~~=~~"xtra">PMID:021645853</ref>~~<references ~~group="xtra"~~/><~~references~~/>		*[[DNA polymerase\|DNA polymerase]]
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
	[[Category: Patel, D J.]]		[[Category: Patel, D J]]
	[[Category: Rechkoblit, O.]]		[[Category: Rechkoblit, O]]
	[[Category: 1-methylguanine]]		[[Category: 1-methylguanine]]
	[[Category: Dna binding]]		[[Category: Dna binding]]

OCA at 09:11, 19 June 2013

2013-06-19T09:11:32Z

← Older revision		Revision as of 09:11, 19 June 2013
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	~~[[Image:3raq.png\|left\|200px]]~~

	{{STRUCTURE_3raq\| PDB=3raq \| SCENE= }}		{{STRUCTURE_3raq\| PDB=3raq \| SCENE= }}

	===Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion===		===Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion===
			{{ABSTRACT_PUBMED_21645853}}

			==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]

	==About this Structure==		==About this Structure==
	[[3raq]] is a 6 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=3RAQ OCA].		[[3raq]] is a 6 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=3RAQ OCA].

	==~~See Also~~==		==Reference==
	*[[DNA polymerase\|DNA polymerase]]		<ref group="xtra">PMID:021645853</ref><references group="xtra"/><references/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]

OCA at 14:36, 20 October 2012

2012-10-20T14:36:51Z

← Older revision		Revision as of 14:36, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[3raq]] is a 6 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=3RAQ OCA].		[[3raq]] is a 6 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=3RAQ OCA].

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

OCA at 15:42, 26 July 2012

2012-07-26T15:42:26Z

← Older revision		Revision as of 15:42, 26 July 2012
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	[[Image:3raq.~~jpg~~\|left\|200px]]		[[Image:3raq.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3raq", 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.~~
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	{{STRUCTURE_3raq\| PDB=3raq \| SCENE= }}		{{STRUCTURE_3raq\| PDB=3raq \| SCENE= }}

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	==About this Structure==		==About this Structure==
	[[3raq]] is a 6 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=3RAQ OCA].		[[3raq]] is a 6 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=3RAQ OCA].

			==See Also==
			*[[DNA polymerase\|DNA polymerase]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]

OCA at 06:35, 15 June 2011

2011-06-15T06:35:08Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:3raq.jpg|left|200px]]
-The entry 3raq is ON HOLD  until Paper Publication
+<!--
-Authors: Rechkoblit, O., Patel, D.J.
+===Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion===
-Description: Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion

OCA at 10:19, 21 April 2011

2011-04-21T10:19:49Z

← Older revision		Revision as of 10:19, 21 April 2011
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 3raq is ON HOLD		The entry 3raq is ON HOLD until Paper Publication

	Authors: Rechkoblit, O., Patel, D.J.		Authors: Rechkoblit, O., Patel, D.J.

	Description: Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion		Description: Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion

OCA at 04:57, 13 April 2011

2011-04-13T04:57:46Z

← Older revision		Revision as of 04:57, 13 April 2011
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	The entry 3raq is ON HOLD		The entry 3raq is ON HOLD

	Authors: Rechkoblit, O., Patel, D. J.		Authors: Rechkoblit, O., Patel, D.J.

	Description: ~~DPO4 EXTENSION TERNARY COMPLEX WITH~~ 3 -~~TERMINAL PRIMER~~ C ~~BASE OPPOSITE THE~~ 1-~~METHYLGUANINE~~ (~~M1G~~) ~~LESION~~		Description: Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion

OCA: Protected "3raq" [edit=sysop:move=sysop]

2011-04-06T08:41:54Z

Protected "3raq" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:41, 6 April 2011
(No difference)