5cwr - Revision history

OCA at 16:13, 8 November 2023

OCA — Wed, 08 Nov 2023 16:13:09 GMT

←Older revision		Revision as of 16:13, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cwr]] is a 8 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=5CWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CWR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cwr]] is a 8 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=5CWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CWR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</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=5cwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cwr OCA], [https://pdbe.org/5cwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cwr RCSB], [https://www.ebi.ac.uk/pdbsum/5cwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cwr 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=5cwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cwr OCA], [https://pdbe.org/5cwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cwr RCSB], [https://www.ebi.ac.uk/pdbsum/5cwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cwr ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:11, 21 June 2023

OCA — Wed, 21 Jun 2023 10:11:06 GMT

←Older revision		Revision as of 10:11, 21 June 2023
Line 3:		Line 3:
	<StructureSection load='5cwr' size='340' side='right'caption='[[5cwr]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5cwr' size='340' side='right'caption='[[5cwr]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cwr]] is a 8 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=5CWR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CWR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cwr]] is a 8 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=5CWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CWR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cb1\|5cb1]]</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=5cwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cwr OCA], [https://pdbe.org/5cwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cwr RCSB], [https://www.ebi.ac.uk/pdbsum/5cwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cwr ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5cwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cwr OCA], [~~http~~://pdbe.org/5cwr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5cwr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5cwr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5cwr 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 28:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Liu, M S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Tsai, M D~~]]	+	[[Category: Liu MS]]
-	[[Category: ~~Polymerase lambda]]~~	+	[[Category: Tsai MD]]
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 10:27, 1 April 2020

OCA — Wed, 01 Apr 2020 10:27:47 GMT

←Older revision		Revision as of 10:27, 1 April 2020
Line 1:		Line 1:

	==Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP==		==Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP==
-	<StructureSection load='5cwr' size='340' side='right' caption='[[5cwr]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5cwr' size='340' side='right'caption='[[5cwr]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cwr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CWR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cwr]] is a 8 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=5CWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CWR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cb1\|5cb1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cb1\|5cb1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5cwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cwr OCA], [http://pdbe.org/5cwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cwr RCSB], [http://www.ebi.ac.uk/pdbsum/5cwr 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=5cwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cwr OCA], [http://pdbe.org/5cwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cwr RCSB], [http://www.ebi.ac.uk/pdbsum/5cwr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cwr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5cwr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5cwr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Liu, M S]]		[[Category: Liu, M S]]
	[[Category: Tsai, M D]]		[[Category: Tsai, M D]]

OCA at 18:11, 26 February 2016

OCA — Fri, 26 Feb 2016 18:11:38 GMT

←Older revision		Revision as of 18:11, 26 February 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5cwr is ~~ON HOLD~~ ~~until Jul 28 2017~~	+	==Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP==
		+	<StructureSection load='5cwr' size='340' side='right' caption='[[5cwr]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5cwr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CWR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cb1\|5cb1]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5cwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cwr OCA], [http://pdbe.org/5cwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cwr RCSB], [http://www.ebi.ac.uk/pdbsum/5cwr PDBsum]</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 ==
		+	The mechanism of DNA polymerase (pol) fidelity is of fundamental importance in chemistry and biology. While high-fidelity pols have been well studied, much less is known about how some pols achieve medium or low fidelity with functional importance. Here we examine how human DNA polymerase lambda (Pol lambda) achieves medium fidelity by determining 12 crystal structures and performing pre-steady-state kinetic analyses. We showed that apo-Pol lambda exists in the closed conformation, unprecedentedly with a preformed MgdNTP binding pocket, and binds MgdNTP readily in the active conformation in the absence of DNA. Since prebinding of MgdNTP could lead to very low fidelity as shown previously, it is attenuated in Pol lambda by a hydrophobic core including Leu431, Ile492, and the Tyr505/Phe506 motif. We then predicted and demonstrated that L431A mutation enhances MgdNTP prebinding and lowers the fidelity. We also hypothesized that the MgdNTP-prebinding ability could stabilize a mismatched ternary complex and destabilize a matched ternary complex, and provided evidence with structures in both forms. Our results demonstrate that, while high-fidelity pols follow a common paradigm, Pol lambda has developed specific conformations and mechanisms for its medium fidelity. Structural comparison with other pols also suggests that different pols likely utilize different conformational changes and microscopic mechanisms to achieve their catalytic functions with varying fidelities.

-	~~Authors: Liu, M.S~~., Tsai, M.D.	+	Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda.,Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD J Am Chem Soc. 2016 Feb 24;138(7):2389-98. doi: 10.1021/jacs.5b13368. Epub 2016, Feb 11. PMID:26836966<ref>PMID:26836966</ref>

-	~~Description: Crystal Structure~~ of ~~human~~ DNA ~~polymerase lambda L431A mutant in complex with a one nucleotide~~ DNA ~~gap and dCTP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Tsai, M.D]]	+	<div class="pdbe-citations 5cwr" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Liu, M.S~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Liu, M S]]
		+	[[Category: Tsai, M D]]
		+	[[Category: Polymerase lambda]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-dna complex]]

OCA at 10:45, 16 December 2015

OCA — Wed, 16 Dec 2015 10:45:29 GMT

←Older revision		Revision as of 10:45, 16 December 2015
Line 7:		Line 7:
	Description: Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP		Description: Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Liu, M.S]]
	[[Category: Tsai, M.D]]		[[Category: Tsai, M.D]]
		+	[[Category: Liu, M.S]]

OCA at 12:28, 30 September 2015

OCA — Wed, 30 Sep 2015 12:28:28 GMT

←Older revision		Revision as of 12:28, 30 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5cwr is ON HOLD	+	The entry 5cwr is ON HOLD until Jul 28 2017

	Authors: Liu, M.S., Tsai, M.D.		Authors: Liu, M.S., Tsai, M.D.

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

OCA — Wed, 05 Aug 2015 19:04:20 GMT

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

←Older revision

Revision as of 19:04, 5 August 2015

OCA: New page: '''Unreleased structure''' The entry 5cwr is ON HOLD Authors: Liu, M.S., Tsai, M.D. Description: Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nuc...

OCA — Wed, 05 Aug 2015 19:04:18 GMT

New page: '''Unreleased structure''' The entry 5cwr is ON HOLD Authors: Liu, M.S., Tsai, M.D. Description: Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nuc...

New page

'''Unreleased structure'''

The entry 5cwr is ON HOLD

Authors: Liu, M.S., Tsai, M.D.

Description: Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP
[[Category: Unreleased Structures]]
[[Category: Liu, M.S]]
[[Category: Tsai, M.D]]