5j0w - Revision history

OCA at 10:41, 6 September 2023

OCA — Wed, 06 Sep 2023 10:41:35 GMT

←Older revision		Revision as of 10:41, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5j0w' size='340' side='right'caption='[[5j0w]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5j0w' size='340' side='right'caption='[[5j0w]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j0w]] 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=5J0W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J0W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j0w]] 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=5J0W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J0W 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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[5j0o\|5j0o]], [[5j0p\|5j0p]], [[5j0q\|5j0q]], [[5j0r\|5j0r]], [[5j0s\|5j0s]], [[5j0t\|5j0t]], [[5j0u\|5j0u]], [[5j0v\|5j0v]], [[5j0x\|5j0x]], [[5j0y\|5j0y]], [[5j29\|5j29]], [[5j2a\|5j2a]], [[5j2b\|5j2b]], [[5j2c\|5j2c]], [[5j2d\|5j2d]], [[5j2e\|5j2e]], [[5j2f\|5j2f]], [[5j2g\|5j2g]], [[5j2h\|5j2h]], [[5j2i\|5j2i]], [[5j2j\|5j2j]], [[5j2k\|5j2k]]</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~~='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'>[https://proteopedia.org/fgij/fg.htm?mol=5j0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0w OCA], [https://pdbe.org/5j0w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j0w RCSB], [https://www.ebi.ac.uk/pdbsum/5j0w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0w ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5j0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0w OCA], [~~http~~://pdbe.org/5j0w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j0w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j0w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0w 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 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Batra, V K~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Wilson, S H~~]]	+	[[Category: Batra VK]]
-	[[Category: ~~Binary complex]]~~	+	[[Category: Wilson SH]]
-	~~[[Category: Dna polymerase beta]]~~	+
-	~~[[Category: Mismatch extension]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 07:24, 10 June 2020

OCA — Wed, 10 Jun 2020 07:24:15 GMT

←Older revision		Revision as of 07:24, 10 June 2020
Line 1:		Line 1:

	==Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus==		==Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus==
-	<StructureSection load='5j0w' size='340' side='right' caption='[[5j0w]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5j0w' size='340' side='right'caption='[[5j0w]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j0w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J0W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J0W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j0w]] 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=5J0W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J0W 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">[[5j0o\|5j0o]], [[5j0p\|5j0p]], [[5j0q\|5j0q]], [[5j0r\|5j0r]], [[5j0s\|5j0s]], [[5j0t\|5j0t]], [[5j0u\|5j0u]], [[5j0v\|5j0v]], [[5j0x\|5j0x]], [[5j0y\|5j0y]], [[5j29\|5j29]], [[5j2a\|5j2a]], [[5j2b\|5j2b]], [[5j2c\|5j2c]], [[5j2d\|5j2d]], [[5j2e\|5j2e]], [[5j2f\|5j2f]], [[5j2g\|5j2g]], [[5j2h\|5j2h]], [[5j2i\|5j2i]], [[5j2j\|5j2j]], [[5j2k\|5j2k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j0o\|5j0o]], [[5j0p\|5j0p]], [[5j0q\|5j0q]], [[5j0r\|5j0r]], [[5j0s\|5j0s]], [[5j0t\|5j0t]], [[5j0u\|5j0u]], [[5j0v\|5j0v]], [[5j0x\|5j0x]], [[5j0y\|5j0y]], [[5j29\|5j29]], [[5j2a\|5j2a]], [[5j2b\|5j2b]], [[5j2c\|5j2c]], [[5j2d\|5j2d]], [[5j2e\|5j2e]], [[5j2f\|5j2f]], [[5j2g\|5j2g]], [[5j2h\|5j2h]], [[5j2i\|5j2i]], [[5j2j\|5j2j]], [[5j2k\|5j2k]]</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=5j0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0w OCA], [http://pdbe.org/5j0w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0w RCSB], [http://www.ebi.ac.uk/pdbsum/5j0w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0w 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://proteopedia.org/fgij/fg.htm?mol=5j0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0w OCA], [http://pdbe.org/5j0w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0w RCSB], [http://www.ebi.ac.uk/pdbsum/5j0w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5j0w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5j0w" 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: Large Structures]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Wilson, S H]]		[[Category: Wilson, S H]]

OCA at 18:26, 26 October 2016

OCA — Wed, 26 Oct 2016 18:26:36 GMT

←Older revision		Revision as of 18:26, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j0w is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus==
		+	<StructureSection load='5j0w' size='340' side='right' caption='[[5j0w]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5j0w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J0W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J0W 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">[[5j0o\|5j0o]], [[5j0p\|5j0p]], [[5j0q\|5j0q]], [[5j0r\|5j0r]], [[5j0s\|5j0s]], [[5j0t\|5j0t]], [[5j0u\|5j0u]], [[5j0v\|5j0v]], [[5j0x\|5j0x]], [[5j0y\|5j0y]], [[5j29\|5j29]], [[5j2a\|5j2a]], [[5j2b\|5j2b]], [[5j2c\|5j2c]], [[5j2d\|5j2d]], [[5j2e\|5j2e]], [[5j2f\|5j2f]], [[5j2g\|5j2g]], [[5j2h\|5j2h]], [[5j2i\|5j2i]], [[5j2j\|5j2j]], [[5j2k\|5j2k]]</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=5j0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0w OCA], [http://pdbe.org/5j0w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0w RCSB], [http://www.ebi.ac.uk/pdbsum/5j0w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0w ProSAT]</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 ==
		+	High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase beta with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis.

-	~~Authors:~~ Batra, V.K., ~~Wilson, S~~.H.	+	Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.,Batra VK, Beard WA, Pedersen LC, Wilson SH Structure. 2016 Sep 13. pii: S0969-2126(16)30238-6. doi:, 10.1016/j.str.2016.08.006. PMID:27642161<ref>PMID:27642161</ref>

-	~~Description: Binary complex crystal structure~~ of ~~DNA polymerase Beta with T:C mismatch at~~ the ~~primer terminus~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Wilson, S.H]]	+	<div class="pdbe-citations 5j0w" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Batra, V.K~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Batra, V K]]
		+	[[Category: Wilson, S H]]
		+	[[Category: Binary complex]]
		+	[[Category: Dna polymerase beta]]
		+	[[Category: Mismatch extension]]
		+	[[Category: Transferase-dna complex]]

OCA at 13:01, 1 June 2016

OCA — Wed, 01 Jun 2016 13:01:20 GMT

←Older revision		Revision as of 13:01, 1 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j0w is ON HOLD	+	The entry 5j0w is ON HOLD until Paper Publication

	Authors: Batra, V.K., Wilson, S.H.		Authors: Batra, V.K., Wilson, S.H.

OCA: Protected "5j0w" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:16:43 GMT

Protected "5j0w" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:16, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j0w is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the pr...

OCA — Wed, 11 May 2016 01:16:42 GMT

New page: '''Unreleased structure''' The entry 5j0w is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the pr...

New page

'''Unreleased structure'''

The entry 5j0w is ON HOLD

Authors: Batra, V.K., Wilson, S.H.

Description: Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus
[[Category: Unreleased Structures]]
[[Category: Wilson, S.H]]
[[Category: Batra, V.K]]