5dbb - Revision history

OCA at 12:23, 6 March 2024

OCA — Wed, 06 Mar 2024 12:23:39 GMT

←Older revision		Revision as of 12:23, 6 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dbb]] 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=5DBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DBB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dbb]] 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=5DBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DBB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.25Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=5dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbb OCA], [https://pdbe.org/5dbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dbb RCSB], [https://www.ebi.ac.uk/pdbsum/5dbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbb 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=5dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbb OCA], [https://pdbe.org/5dbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dbb RCSB], [https://www.ebi.ac.uk/pdbsum/5dbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbb 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 ==
-	N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polbeta-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polbeta-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.
-
-	N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA.,Kou Y, Koag MC, Lee S J Am Chem Soc. 2015 Nov 11;137(44):14067-70. doi: 10.1021/jacs.5b10172. Epub 2015, Nov 2. PMID:26517568<ref>PMID:26517568</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5dbb" style="background-color:#fffaf0;"></div>

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

OCA at 10:29, 21 June 2023

OCA — Wed, 21 Jun 2023 10:29:12 GMT

←Older revision		Revision as of 10:29, 21 June 2023
Line 1:		Line 1:

	==Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA==		==Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA==
-	<StructureSection load='5dbb' size='340' side='right' caption='[[5dbb]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='5dbb' size='340' side='right'caption='[[5dbb]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dbb]] 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=5DBB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dbb]] 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=5DBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DBB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5db6\|5db6]], [[5db7\|5db7]], [[5db8\|5db8]], [[5db9\|5db9]], [[5dba\|5dba]], [[5dbc\|5dbc]]</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=5dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbb OCA], [https://pdbe.org/5dbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dbb RCSB], [https://www.ebi.ac.uk/pdbsum/5dbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbb ProSAT]</span></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=5dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbb OCA], [~~http~~://pdbe.org/5dbb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dbb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dbb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbb 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 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5dbb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dbb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== 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 MC]]
-	[[Category: ~~Human dna polymerase]]~~	+	[[Category: Lee S]]
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 14:07, 16 November 2017

OCA — Thu, 16 Nov 2017 14:07:26 GMT

←Older revision		Revision as of 14:07, 16 November 2017
Line 1:		Line 1:
		+
	==Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA==		==Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA==
	<StructureSection load='5dbb' size='340' side='right' caption='[[5dbb]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='5dbb' size='340' side='right' caption='[[5dbb]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dbb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dbb]] 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=5DBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DBB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5db6\|5db6]], [[5db7\|5db7]], [[5db8\|5db8]], [[5db9\|5db9]], [[5dba\|5dba]], [[5dbc\|5dbc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5db6\|5db6]], [[5db7\|5db7]], [[5db8\|5db8]], [[5db9\|5db9]], [[5dba\|5dba]], [[5dbc\|5dbc]]</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=5dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbb OCA], [http://pdbe.org/5dbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dbb RCSB], [http://www.ebi.ac.uk/pdbsum/5dbb PDBsum]</span></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=5dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbb OCA], [http://pdbe.org/5dbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dbb RCSB], [http://www.ebi.ac.uk/pdbsum/5dbb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Koag, M C]]		[[Category: Koag, M C]]
	[[Category: Lee, S]]		[[Category: Lee, S]]
	[[Category: Human dna polymerase]]		[[Category: Human dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 21:37, 30 November 2015

OCA — Mon, 30 Nov 2015 21:37:59 GMT

←Older revision		Revision as of 21:37, 30 November 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA==
		+	<StructureSection load='5dbb' size='340' side='right' caption='[[5dbb]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dbb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DBB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5db6\|5db6]], [[5db7\|5db7]], [[5db8\|5db8]], [[5db9\|5db9]], [[5dba\|5dba]], [[5dbc\|5dbc]]</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=5dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbb OCA], [http://pdbe.org/5dbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dbb RCSB], [http://www.ebi.ac.uk/pdbsum/5dbb PDBsum]</span></td></tr>
		+	</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;">
		+	== Publication Abstract from PubMed ==
		+	N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polbeta-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polbeta-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.

-	~~The entry 5dbb is ON HOLD until Paper Publication~~	+	N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA.,Kou Y, Koag MC, Lee S J Am Chem Soc. 2015 Nov 11;137(44):14067-70. doi: 10.1021/jacs.5b10172. Epub 2015, Nov 2. PMID:26517568<ref>PMID:26517568</ref>

-	~~Authors: Koag~~, M.~~C., Lee,~~ S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Structure of human DNA polymerase beta Host~~-~~Guest complex with the dG base paired with a dA~~	+	<div class="pdbe-citations 5dbb" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
-	[[Category: Koag, M.C]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Koag, M C]]
	[[Category: Lee, S]]		[[Category: Lee, S]]
		+	[[Category: Human dna polymerase]]
		+	[[Category: Transferase-dna complex]]

OCA at 12:50, 30 September 2015

OCA — Wed, 30 Sep 2015 12:50:46 GMT

←Older revision		Revision as of 12:50, 30 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5dbb is ON HOLD	+	The entry 5dbb is ON HOLD until Paper Publication

	Authors: Koag, M.C., Lee, S.		Authors: Koag, M.C., Lee, S.

OCA at 11:24, 2 September 2015

OCA — Wed, 02 Sep 2015 11:24:06 GMT

←Older revision		Revision as of 11:24, 2 September 2015
Line 3:		Line 3:
	The entry 5dbb is ON HOLD		The entry 5dbb is ON HOLD

-	Authors: ~~koag~~, m.c., ~~lee~~, s	+	Authors: Koag, M.C., Lee, S.

	Description: Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA		Description: Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA

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

OCA — Wed, 26 Aug 2015 12:42:25 GMT

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

←Older revision

Revision as of 12:42, 26 August 2015

OCA: New page: '''Unreleased structure''' The entry 5dbb is ON HOLD Authors: koag, m.c., lee, s Description: Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a d...

OCA — Wed, 26 Aug 2015 12:42:24 GMT

New page: '''Unreleased structure''' The entry 5dbb is ON HOLD Authors: koag, m.c., lee, s Description: Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a d...

New page

'''Unreleased structure'''

The entry 5dbb is ON HOLD

Authors: koag, m.c., lee, s

Description: Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA
[[Category: Unreleased Structures]]
[[Category: Koag, M.C]]
[[Category: Lee, S]]