6bte - Revision history

OCA at 14:49, 4 October 2023

2023-10-04T14:49:55Z

←Older revision		Revision as of 14:49, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6bte' size='340' side='right'caption='[[6bte]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6bte' size='340' side='right'caption='[[6bte]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bte]] 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=6BTE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BTE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bte]] 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=6BTE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BTE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 2.2Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bte OCA], [~~http~~://pdbe.org/6bte PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bte RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bte PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bte 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=6bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bte OCA], [https://pdbe.org/6bte PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bte RCSB], [https://www.ebi.ac.uk/pdbsum/6bte PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bte 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 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Doublie, S]]	+	[[Category: Doublie S]]
-	[[Category: Eckenroth~~, B E]]~~	+	[[Category: Eckenroth BE]]
-	~~[[Category: Dna complex]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Lyase-dna complex]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:55, 4 December 2019

2019-12-04T09:55:08Z

←Older revision		Revision as of 09:55, 4 December 2019
Line 1:		Line 1:

	==DNA Polymerase Beta I260Q Binary Complex==		==DNA Polymerase Beta I260Q Binary Complex==
-	<StructureSection load='6bte' size='340' side='right' caption='[[6bte]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='6bte' size='340' side='right'caption='[[6bte]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bte]] 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=6BTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTE FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bte]] 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=6BTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTE FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6bte" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bte" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Doublie, S]]		[[Category: Doublie, S]]
	[[Category: Eckenroth, B E]]		[[Category: Eckenroth, B E]]

OCA at 08:40, 3 October 2018

2018-10-03T08:40:51Z

←Older revision		Revision as of 08:40, 3 October 2018
Line 3:		Line 3:
	<StructureSection load='6bte' size='340' side='right' caption='[[6bte]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6bte' size='340' side='right' caption='[[6bte]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bte]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bte]] 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=6BTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=6bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bte OCA], [http://pdbe.org/6bte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bte RCSB], [http://www.ebi.ac.uk/pdbsum/6bte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bte 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=6bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bte OCA], [http://pdbe.org/6bte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bte RCSB], [http://www.ebi.ac.uk/pdbsum/6bte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bte 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>		[[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 ==
		+	DNA polymerase beta (pol beta) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol beta must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol beta's ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol beta to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol beta.
		+
		+	I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.,Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S, Loria JP, Sweasy JB Nucleic Acids Res. 2018 Sep 17. pii: 5098607. doi: 10.1093/nar/gky825. PMID:30239932<ref>PMID:30239932</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6bte" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Doublie, S]]		[[Category: Doublie, S]]
	[[Category: Eckenroth, B E]]		[[Category: Eckenroth, B E]]

OCA at 08:01, 26 September 2018

2018-09-26T08:01:55Z

←Older revision		Revision as of 08:01, 26 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bte ~~is ON HOLD until Paper Publication~~	+	==DNA Polymerase Beta I260Q Binary Complex==
-		+	<StructureSection load='6bte' size='340' side='right' caption='[[6bte]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Eckenroth, B~~.E.~~, Doublie, S~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6bte]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTE FirstGlance]. <br>
-	~~Description~~: ~~DNA Polymerase Beta I260Q Binary Complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bte OCA], [http://pdbe.org/6bte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bte RCSB], [http://www.ebi.ac.uk/pdbsum/6bte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bte ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Eckenroth~~, B.E]]	+	</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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Doublie, S]]		[[Category: Doublie, S]]
		+	[[Category: Eckenroth, B E]]
		+	[[Category: Dna complex]]
		+	[[Category: Lyase]]
		+	[[Category: Lyase-dna complex]]
		+	[[Category: Transferase]]

OCA at 17:14, 24 January 2018

2018-01-24T17:14:19Z

←Older revision		Revision as of 17:14, 24 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bte is ON HOLD	+	The entry 6bte is ON HOLD until Paper Publication

	Authors: Eckenroth, B.E., Doublie, S.		Authors: Eckenroth, B.E., Doublie, S.

OCA: Protected "6bte" [edit=sysop:move=sysop]

2017-12-13T05:56:47Z

Protected "6bte" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:56, 13 December 2017

OCA: New page: '''Unreleased structure''' The entry 6bte is ON HOLD Authors: Eckenroth, B.E., Doublie, S. Description: DNA Polymerase Beta I260Q Binary Complex Category: Unreleased Structures [[C...

2017-12-13T05:56:46Z

New page: '''Unreleased structure''' The entry 6bte is ON HOLD Authors: Eckenroth, B.E., Doublie, S. Description: DNA Polymerase Beta I260Q Binary Complex Category: Unreleased Structures [[C...

New page

'''Unreleased structure'''

The entry 6bte is ON HOLD

Authors: Eckenroth, B.E., Doublie, S.

Description: DNA Polymerase Beta I260Q Binary Complex
[[Category: Unreleased Structures]]
[[Category: Eckenroth, B.E]]
[[Category: Doublie, S]]