4ny8 - Revision history

OCA at 12:36, 1 March 2024

OCA — Fri, 01 Mar 2024 12:36:29 GMT

←Older revision		Revision as of 12:36, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ny8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NY8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ny8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NY8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.246Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [https://pdbe.org/4ny8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ny8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ny8 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=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [https://pdbe.org/4ny8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ny8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ny8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>		[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Human DNA polymerase beta (polbeta) inserts, albeit slowly, T opposite the carcinogenic lesion O6-methylguanine (O6MeG) approximately 30-fold more frequently than C. To gain insight into this promutagenic process, we solved four ternary structures of polbeta with an incoming dCTP or dTTP analogue base-paired with O6MeG in the presence of active-site Mg2+ or Mn2+. The Mg2+-bound structures show that both the O6MeG.dCTP/dTTP-Mg2+ complexes adopt an open protein conformation, staggered base pair, and one active-site metal ion. The Mn2+-bound structures reveal that, whereas the O6Me.dCTP-Mn2+ complex assumes the similar altered conformation, the O6MeG.dTTP-Mn2+ complex adopts a catalytically competent state with a closed protein conformation and pseudo-Watson-Crick base pair. On the basis of these observations, we conclude that polbeta slows nucleotide incorporation opposite O6MeG by inducing an altered conformation suboptimal for catalysis and promotes mutagenic replication by allowing Watson-Crick-mode for O6MeG.T but not for O6MeG.C in the enzyme active site. The O6MeG.dTTP-Mn2+ ternary structure, which represents the first structure of mismatched polbeta ternary complex with a closed protein conformation and coplanar base pair, the first structure of pseudo-Watson-Crick O6MeG.T formed in the active site of a DNA polymerase, and a rare, if not the first, example of metal-dependent conformational activation of a DNA polymerase, indicate that catalytic metal-ion coordination is utilized as a kinetic checkpoint by polbeta and is crucial for the conformational activation of polbeta. Overall, our structural studies not only explain the promutagenic polbeta catalysis across O6MeG but also provide new insights into the replication fidelity of polbeta.

-	Metal-Dependent Conformational Activation Explains Highly Promutagenic Replication across O6-Methylguanine by Human DNA Polymerase beta,Koag MC, Lee S J Am Chem Soc. 2014 Apr 2. PMID:24694247<ref>PMID:24694247</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 4ny8" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:45, 18 January 2023

OCA — Wed, 18 Jan 2023 08:45:33 GMT

←Older revision		Revision as of 08:45, 18 January 2023
Line 1:		Line 1:

	==DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site==		==DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site==
-	<StructureSection load='4ny8' size='340' side='right' caption='[[4ny8]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='4ny8' size='340' side='right'caption='[[4ny8]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ny8]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NY8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ny8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NY8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MN:~~MANGANESE~~+~~(II)+ION~~'>MN</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=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=~~6OG~~:~~6-O-METHYL~~+~~GUANOSINE-5-MONOPHOSPHATE~~'>~~6OG~~</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=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [https://pdbe.org/4ny8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ny8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ny8 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nxz\|4nxz]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [~~http~~://pdbe.org/4ny8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ny8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ny8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>	+	[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	<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 4ny8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ny8" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Koag, M C]]	+	[[Category: Large Structures]]
-	[[Category: Lee, S]]	+	[[Category: Koag M-C]]
-	[[Category: Min, K]]	+	[[Category: Lee S]]
-	[[Category: Monzingo~~, A F]]~~	+	[[Category: Min K]]
-	~~[[Category: Dna binding]]~~	+	[[Category: Monzingo AF]]
-	~~[[Category: Dna polymerase fold]]~~	+
-	~~[[Category: Lyase-dna complex]]~~	+
-	~~[[Category: Nucleolus]]~~	+
-	~~[[Category: Nucleotidyl transfer]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 04:20, 5 August 2016

OCA — Fri, 05 Aug 2016 04:20:09 GMT

←Older revision		Revision as of 04:20, 5 August 2016
Line 1:		Line 1:
		+
	==DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site==		==DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site==
	<StructureSection load='4ny8' size='340' side='right' caption='[[4ny8]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='4ny8' size='340' side='right' caption='[[4ny8]], [[Resolution\|resolution]] 2.25Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nxz\|4nxz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nxz\|4nxz]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ny8 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=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [http://pdbe.org/4ny8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ny8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ny8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4ny8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:46, 25 December 2014

OCA — Thu, 25 Dec 2014 15:46:39 GMT

←Older revision		Revision as of 15:46, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ny8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NY8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ny8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NY8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nxz\|4nxz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nxz\|4nxz]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ny8 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=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ny8 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Koag, M C.]]	+	[[Category: Koag, M C]]
-	[[Category: Lee, S.]]	+	[[Category: Lee, S]]
-	[[Category: Min, K.]]	+	[[Category: Min, K]]
-	[[Category: Monzingo, A F.]]	+	[[Category: Monzingo, A F]]
	[[Category: Dna binding]]		[[Category: Dna binding]]
	[[Category: Dna polymerase fold]]		[[Category: Dna polymerase fold]]

OCA at 06:19, 2 July 2014

OCA — Wed, 02 Jul 2014 06:19:49 GMT

←Older revision		Revision as of 06:19, 2 July 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4ny8\| PDB=4ny8 \| SCENE= }}~~	+	==DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site==
-	===DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site===	+	<StructureSection load='4ny8' size='340' side='right' caption='[[4ny8]], [[Resolution\|resolution]] 2.25Å' scene=''>
-	{~~{ABSTRACT_PUBMED_24694247}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ny8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NY8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nxz\|4nxz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ny8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ny8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ny8 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human DNA polymerase beta (polbeta) inserts, albeit slowly, T opposite the carcinogenic lesion O6-methylguanine (O6MeG) approximately 30-fold more frequently than C. To gain insight into this promutagenic process, we solved four ternary structures of polbeta with an incoming dCTP or dTTP analogue base-paired with O6MeG in the presence of active-site Mg2+ or Mn2+. The Mg2+-bound structures show that both the O6MeG.dCTP/dTTP-Mg2+ complexes adopt an open protein conformation, staggered base pair, and one active-site metal ion. The Mn2+-bound structures reveal that, whereas the O6Me.dCTP-Mn2+ complex assumes the similar altered conformation, the O6MeG.dTTP-Mn2+ complex adopts a catalytically competent state with a closed protein conformation and pseudo-Watson-Crick base pair. On the basis of these observations, we conclude that polbeta slows nucleotide incorporation opposite O6MeG by inducing an altered conformation suboptimal for catalysis and promotes mutagenic replication by allowing Watson-Crick-mode for O6MeG.T but not for O6MeG.C in the enzyme active site. The O6MeG.dTTP-Mn2+ ternary structure, which represents the first structure of mismatched polbeta ternary complex with a closed protein conformation and coplanar base pair, the first structure of pseudo-Watson-Crick O6MeG.T formed in the active site of a DNA polymerase, and a rare, if not the first, example of metal-dependent conformational activation of a DNA polymerase, indicate that catalytic metal-ion coordination is utilized as a kinetic checkpoint by polbeta and is crucial for the conformational activation of polbeta. Overall, our structural studies not only explain the promutagenic polbeta catalysis across O6MeG but also provide new insights into the replication fidelity of polbeta.

-	~~==Function==~~	+	Metal-Dependent Conformational Activation Explains Highly Promutagenic Replication across O6-Methylguanine by Human DNA Polymerase beta,Koag MC, Lee S J Am Chem Soc. 2014 Apr 2. PMID:24694247<ref>PMID:24694247</ref>
-	~~[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base~~-~~excision repair. Has 5'~~-~~deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a~~ DNA ~~polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap~~. ~~Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases~~.~~<ref>~~PMID:~~9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref>~~ <ref>PMID:~~21362556~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4ny8]] is~~ a ~~4 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4NY8 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024694247</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
	[[Category: Koag, M C.]]		[[Category: Koag, M C.]]
	[[Category: Lee, S.]]		[[Category: Lee, S.]]

OCA at 09:41, 16 April 2014

OCA — Wed, 16 Apr 2014 09:41:47 GMT

←Older revision		Revision as of 09:41, 16 April 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4ny8\| PDB=4ny8 \| SCENE= }}
		+	===DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site===
		+	{{ABSTRACT_PUBMED_24694247}}

-	~~The entry 4ny8 is ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>

-	~~Authors~~: ~~Koag, M~~.-C.~~, Min, K~~.~~, Monzingo, A.F., Lee, S~~.	+	==About this Structure==
		+	[[4ny8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NY8 OCA].

-	~~Description~~: ~~DNA~~ polymerase ~~beta with O6mG in the template base opposite to incoming non~~-~~hydrolyzable CTP with manganese in the active site~~	+	==Reference==
		+	<ref group="xtra">PMID:024694247</ref><references group="xtra"/><references/>
		+	[[Category: Koag, M C.]]
		+	[[Category: Lee, S.]]
		+	[[Category: Min, K.]]
		+	[[Category: Monzingo, A F.]]
		+	[[Category: Dna binding]]
		+	[[Category: Dna polymerase fold]]
		+	[[Category: Lyase-dna complex]]
		+	[[Category: Nucleolus]]
		+	[[Category: Nucleotidyl transfer]]
		+	[[Category: Transferase]]

OCA at 06:45, 22 January 2014

OCA — Wed, 22 Jan 2014 06:45:11 GMT

←Older revision		Revision as of 06:45, 22 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ny8 is ON HOLD	+	The entry 4ny8 is ON HOLD until Paper Publication

	Authors: Koag, M.-C., Min, K., Monzingo, A.F., Lee, S.		Authors: Koag, M.-C., Min, K., Monzingo, A.F., Lee, S.

	Description: DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site		Description: DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site

OCA at 07:38, 15 January 2014

OCA — Wed, 15 Jan 2014 07:38:46 GMT

←Older revision		Revision as of 07:38, 15 January 2014
Line 3:		Line 3:
	The entry 4ny8 is ON HOLD		The entry 4ny8 is ON HOLD

-	Authors: Koag, M-C., Min, K, Monzingo, A.F., Lee, S	+	Authors: Koag, M.-C., Min, K., Monzingo, A.F., Lee, S.

-	Description: DNA ~~POLYMERASE BETA WITH O6MG~~ in the template base opposite to incoming non-hydrolyzable CTP ~~WITH MANGANESE IN THE ACTIVE SITE~~	+	Description: DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site

OCA: Protected "4ny8" [edit=sysop:move=sysop]

OCA — Wed, 18 Dec 2013 09:27:01 GMT

Protected "4ny8" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:27, 18 December 2013

OCA: New page: '''Unreleased structure''' The entry 4ny8 is ON HOLD Authors: Koag, M-C., Min, K, Monzingo, A.F., Lee, S Description: DNA POLYMERASE BETA WITH O6MG in the template base opposite to inc...

OCA — Wed, 18 Dec 2013 09:27:00 GMT

New page: '''Unreleased structure''' The entry 4ny8 is ON HOLD Authors: Koag, M-C., Min, K, Monzingo, A.F., Lee, S Description: DNA POLYMERASE BETA WITH O6MG in the template base opposite to inc...

New page

'''Unreleased structure'''

The entry 4ny8 is ON HOLD

Authors: Koag, M-C., Min, K, Monzingo, A.F., Lee, S

Description: DNA POLYMERASE BETA WITH O6MG in the template base opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE