4x5v - Revision history

OCA at 12:59, 1 March 2024

OCA — Fri, 01 Mar 2024 12:59:55 GMT

←Older revision		Revision as of 12:59, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=4X5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X5V FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=4X5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X5V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4x5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x5v OCA], [https://pdbe.org/4x5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x5v RCSB], [https://www.ebi.ac.uk/pdbsum/4x5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x5v 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=4x5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x5v OCA], [https://pdbe.org/4x5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x5v RCSB], [https://www.ebi.ac.uk/pdbsum/4x5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x5v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>		[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	8-Oxo-7,8,-dihydro-2'-deoxyguanosine triphosphate (8-oxo-dGTP) is a major product of oxidative damage in the nucleotide pool. It is capable of mispairing with adenosine (dA), resulting in futile, mutagenic cycles of base excision repair. Therefore, it is critical that DNA polymerases discriminate against 8-oxo-dGTP at the insertion step. Because of its roles in oxidative DNA damage repair and non-homologous end joining, DNA polymerase lambda (Pol lambda) may frequently encounter 8-oxo-dGTP. Here, we have studied the mechanisms of 8-oxo-dGMP incorporation and discrimination by Pol lambda. We have solved high resolution crystal structures showing how Pol lambda accommodates 8-oxo-dGTP in its active site. The structures indicate that when mispaired with dA, the oxidized nucleotide assumes the mutagenic syn-conformation, and is stabilized by multiple interactions. Steady-state kinetics reveal that two residues lining the dNTP binding pocket, Ala(510) and Asn(513), play differential roles in dNTP selectivity. Specifically, Ala(510) and Asn(513) facilitate incorporation of 8-oxo-dGMP opposite dA and dC, respectively. These residues also modulate the balance between purine and pyrimidine incorporation. Our results shed light on the mechanisms controlling 8-oxo-dGMP incorporation in Pol lambda and on the importance of interactions with the incoming dNTP to determine selectivity in family X DNA polymerases.
-
-	Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda.,Burak MJ, Guja KE, Garcia-Diaz M Nucleic Acids Res. 2015 Sep 18;43(16):8089-99. doi: 10.1093/nar/gkv760. Epub 2015, Jul 28. PMID:26220180<ref>PMID:26220180</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4x5v" style="background-color:#fffaf0;"></div>

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

OCA at 21:14, 12 April 2023

OCA — Wed, 12 Apr 2023 21:14:38 GMT

←Older revision		Revision as of 21:14, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4x5v' size='340' side='right'caption='[[4x5v]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='4x5v' size='340' side='right'caption='[[4x5v]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X5V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=4X5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X5V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CIT~~:~~CITRIC+ACID~~'>~~CIT~~</scene>, <scene name='pdbligand=MG:~~MAGNESIUM~~+~~ION~~'>MG</scene>, <scene name='pdbligand=NA:~~SODIUM~~+ION'>NA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~8OG~~:~~8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE~~'>~~8OG~~</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=4x5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x5v OCA], [https://pdbe.org/4x5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x5v RCSB], [https://www.ebi.ac.uk/pdbsum/4x5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x5v 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=4x5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x5v OCA], [~~http~~://pdbe.org/4x5v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x5v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x5v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x5v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN]] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>	+	[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4x5v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x5v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Burak, M J~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Garcia-Diaz, M~~]]	+	[[Category: Burak MJ]]
-	[[Category: ~~Guja, K E]]~~	+	[[Category: Garcia-Diaz M]]
-	~~[[Category: Dna polymerase lambda]]~~	+	[[Category: Guja KE]]
-	~~[[Category: Helix~~-~~hairpin-helix~~]]	+
-	[[Category: ~~Protein-dna complex]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 07:18, 29 May 2019

OCA — Wed, 29 May 2019 07:18:48 GMT

←Older revision		Revision as of 07:18, 29 May 2019
Line 1:		Line 1:

	==Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP==		==Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP==
-	<StructureSection load='4x5v' size='340' side='right' caption='[[4x5v]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='4x5v' size='340' side='right'caption='[[4x5v]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X5V FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X5V FirstGlance]. <br>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Burak, M J]]		[[Category: Burak, M J]]
	[[Category: Garcia-Diaz, M]]		[[Category: Garcia-Diaz, M]]

OCA at 16:48, 18 August 2017

OCA — Fri, 18 Aug 2017 16:48:28 GMT

←Older revision		Revision as of 16:48, 18 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4x5v is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP==
		+	<StructureSection load='4x5v' size='340' side='right' caption='[[4x5v]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X5V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></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=4x5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x5v OCA], [http://pdbe.org/4x5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x5v RCSB], [http://www.ebi.ac.uk/pdbsum/4x5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x5v ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN]] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	8-Oxo-7,8,-dihydro-2'-deoxyguanosine triphosphate (8-oxo-dGTP) is a major product of oxidative damage in the nucleotide pool. It is capable of mispairing with adenosine (dA), resulting in futile, mutagenic cycles of base excision repair. Therefore, it is critical that DNA polymerases discriminate against 8-oxo-dGTP at the insertion step. Because of its roles in oxidative DNA damage repair and non-homologous end joining, DNA polymerase lambda (Pol lambda) may frequently encounter 8-oxo-dGTP. Here, we have studied the mechanisms of 8-oxo-dGMP incorporation and discrimination by Pol lambda. We have solved high resolution crystal structures showing how Pol lambda accommodates 8-oxo-dGTP in its active site. The structures indicate that when mispaired with dA, the oxidized nucleotide assumes the mutagenic syn-conformation, and is stabilized by multiple interactions. Steady-state kinetics reveal that two residues lining the dNTP binding pocket, Ala(510) and Asn(513), play differential roles in dNTP selectivity. Specifically, Ala(510) and Asn(513) facilitate incorporation of 8-oxo-dGMP opposite dA and dC, respectively. These residues also modulate the balance between purine and pyrimidine incorporation. Our results shed light on the mechanisms controlling 8-oxo-dGMP incorporation in Pol lambda and on the importance of interactions with the incoming dNTP to determine selectivity in family X DNA polymerases.

-	~~Authors: Burak, M.J~~., Guja~~, K.E.~~, Garcia-Diaz, M.	+	Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda.,Burak MJ, Guja KE, Garcia-Diaz M Nucleic Acids Res. 2015 Sep 18;43(16):8089-99. doi: 10.1093/nar/gkv760. Epub 2015, Jul 28. PMID:26220180<ref>PMID:26220180</ref>

-	~~Description:~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Guja, K.E]]~~	+	<div class="pdbe-citations 4x5v" style="background-color:#fffaf0;"></div>
-	[[Category: Burak, M.J]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Burak, M J]]
	[[Category: Garcia-Diaz, M]]		[[Category: Garcia-Diaz, M]]
		+	[[Category: Guja, K E]]
		+	[[Category: Dna polymerase lambda]]
		+	[[Category: Helix-hairpin-helix]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Transferase-dna complex]]

OCA at 13:48, 31 December 2014

OCA — Wed, 31 Dec 2014 13:48:17 GMT

←Older revision		Revision as of 13:48, 31 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4x5v is ON HOLD	+	The entry 4x5v is ON HOLD until Paper Publication

	Authors: Burak, M.J., Guja, K.E., Garcia-Diaz, M.		Authors: Burak, M.J., Guja, K.E., Garcia-Diaz, M.

OCA at 20:32, 24 December 2014

OCA — Wed, 24 Dec 2014 20:32:06 GMT

←Older revision		Revision as of 20:32, 24 December 2014
Line 5:		Line 5:
	Authors: Burak, M.J., Guja, K.E., Garcia-Diaz, M.		Authors: Burak, M.J., Guja, K.E., Garcia-Diaz, M.

-	Description:	+	Description:
		+	[[Category: Unreleased Structures]]
		+	[[Category: Guja, K.E]]
		+	[[Category: Burak, M.J]]
		+	[[Category: Garcia-Diaz, M]]

OCA: Protected "4x5v" [edit=sysop:move=sysop]

OCA — Wed, 17 Dec 2014 11:42:48 GMT

Protected "4x5v" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:42, 17 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x5v is ON HOLD Authors: Burak, M.J., Guja, K.E., Garcia-Diaz, M. Description:

OCA — Wed, 17 Dec 2014 11:42:47 GMT

New page: '''Unreleased structure''' The entry 4x5v is ON HOLD Authors: Burak, M.J., Guja, K.E., Garcia-Diaz, M. Description:

New page

'''Unreleased structure'''

The entry 4x5v is ON HOLD

Authors: Burak, M.J., Guja, K.E., Garcia-Diaz, M.

Description: