4xrh - Revision history

OCA at 15:30, 8 November 2023

OCA — Wed, 08 Nov 2023 15:30:42 GMT

←Older revision		Revision as of 15:30, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xrh]] 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=4XRH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XRH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xrh]] 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=4XRH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XRH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=4xrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xrh OCA], [https://pdbe.org/4xrh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xrh RCSB], [https://www.ebi.ac.uk/pdbsum/4xrh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xrh 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=4xrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xrh OCA], [https://pdbe.org/4xrh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xrh RCSB], [https://www.ebi.ac.uk/pdbsum/4xrh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xrh ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:48, 26 April 2023

OCA — Wed, 26 Apr 2023 17:48:39 GMT

←Older revision		Revision as of 17:48, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xrh' size='340' side='right'caption='[[4xrh]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4xrh' size='340' side='right'caption='[[4xrh]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xrh]] 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=4XRH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XRH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xrh]] 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=4XRH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XRH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4w5d\|4w5d]]</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=4xrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xrh OCA], [https://pdbe.org/4xrh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xrh RCSB], [https://www.ebi.ac.uk/pdbsum/4xrh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xrh 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=4xrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xrh OCA], [~~http~~://pdbe.org/4xrh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xrh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xrh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xrh 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 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4xrh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xrh" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__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: ~~Dna polymerase lambda]]~~	+	[[Category: Tsai MD]]
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 23:32, 5 June 2019

OCA — Wed, 05 Jun 2019 23:32:24 GMT

←Older revision		Revision as of 23:32, 5 June 2019
Line 1:		Line 1:

	==Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA==		==Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA==
-	<StructureSection load='4xrh' size='340' side='right' caption='[[4xrh]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='4xrh' size='340' side='right'caption='[[4xrh]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xrh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XRH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xrh]] 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=4XRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XRH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4w5d\|4w5d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4w5d\|4w5d]]</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=4xrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xrh OCA], [http://pdbe.org/4xrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xrh RCSB], [http://www.ebi.ac.uk/pdbsum/4xrh 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=4xrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xrh OCA], [http://pdbe.org/4xrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xrh RCSB], [http://www.ebi.ac.uk/pdbsum/4xrh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xrh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 26:
	</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]]
	[[Category: Dna polymerase lambda]]		[[Category: Dna polymerase lambda]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 18:08, 26 February 2016

OCA — Fri, 26 Feb 2016 18:08:59 GMT

←Older revision		Revision as of 18:08, 26 February 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4xrh is ~~ON HOLD~~ ~~until Jul 19 2017~~	+	==Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA==
		+	<StructureSection load='4xrh' size='340' side='right' caption='[[4xrh]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xrh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XRH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4w5d\|4w5d]]</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=4xrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xrh OCA], [http://pdbe.org/4xrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xrh RCSB], [http://www.ebi.ac.uk/pdbsum/4xrh 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~~: ~~Human~~ DNA ~~polymerase lambda~~-~~MgdTTP binary and complex with 6 paired~~ DNA	+	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 4xrh" 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: Dna polymerase lambda]]
		+	[[Category: Transferase-dna complex]]

OCA at 09:52, 20 January 2016

OCA — Wed, 20 Jan 2016 09:52:19 GMT

←Older revision		Revision as of 09:52, 20 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xrh is ON HOLD until ~~Jan 21~~ 2017	+	The entry 4xrh is ON HOLD until Jul 19 2017

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

OCA at 11:09, 2 December 2015

OCA — Wed, 02 Dec 2015 11:09:12 GMT

←Older revision		Revision as of 11:09, 2 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xrh is ON HOLD	+	The entry 4xrh is ON HOLD until Jan 21 2017

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

OCA at 23:17, 30 November 2015

OCA — Mon, 30 Nov 2015 23:17:51 GMT

←Older revision		Revision as of 23:17, 30 November 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xrh is ON HOLD ~~until Jan 21 2017~~	+	The entry 4xrh is ON HOLD

	Authors: Liu, M.S., Tsai, M.D.		Authors: Liu, M.S., Tsai, M.D.
Line 7:		Line 7:
	Description: Human DNA polymerase lambda-MgdTTP binary and complex with 6 paired DNA		Description: Human DNA polymerase lambda-MgdTTP binary and complex with 6 paired DNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Liu, M.S]]
	[[Category: Tsai, M.D]]		[[Category: Tsai, M.D]]
		+	[[Category: Liu, M.S]]

OCA at 10:38, 29 July 2015

OCA — Wed, 29 Jul 2015 10:38:15 GMT

←Older revision		Revision as of 10:38, 29 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xrh is ON HOLD	+	The entry 4xrh is ON HOLD until Jan 21 2017

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

OCA at 10:26, 22 July 2015

OCA — Wed, 22 Jul 2015 10:26:59 GMT

←Older revision		Revision as of 10:26, 22 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xrh is ON HOLD ~~until Jan 21 2017~~	+	The entry 4xrh is ON HOLD

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

OCA at 11:17, 8 July 2015

OCA — Wed, 08 Jul 2015 11:17:33 GMT

←Older revision		Revision as of 11:17, 8 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xrh is ON HOLD	+	The entry 4xrh is ON HOLD until Jan 21 2017

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