5u8i - Revision history

OCA at 13:23, 4 October 2023

OCA — Wed, 04 Oct 2023 13:23:02 GMT

←Older revision		Revision as of 13:23, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5u8i' size='340' side='right'caption='[[5u8i]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5u8i' size='340' side='right'caption='[[5u8i]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u8i]] 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=5U8I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U8I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u8i]] 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=5U8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U8I 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.45Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u8h\|5u8h]]~~, [[~~5u8g~~\|~~5u8g~~]]</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=5u8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8i OCA], [https://pdbe.org/5u8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u8i RCSB], [https://www.ebi.ac.uk/pdbsum/5u8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8i 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=5u8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8i OCA], [~~http~~://pdbe.org/5u8i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u8i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u8i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8i 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: ~~Doublie, S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Eckenroth, B E~~]]	+	[[Category: Doublie S]]
-	[[Category: ~~Dna complex]]~~	+	[[Category: Eckenroth BE]]
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Lyase-dna complex]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:28, 4 December 2019

OCA — Wed, 04 Dec 2019 09:28:32 GMT

←Older revision		Revision as of 09:28, 4 December 2019
Line 1:		Line 1:

	==DNA Polymerase Beta S229L crystallized in PEG 400==		==DNA Polymerase Beta S229L crystallized in PEG 400==
-	<StructureSection load='5u8i' size='340' side='right' caption='[[5u8i]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='5u8i' size='340' side='right'caption='[[5u8i]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5u8i]] 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=5U8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8I FirstGlance]. <br>		<table><tr><td colspan='2'>[[5u8i]] 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=5U8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8I FirstGlance]. <br>
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</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 12:23, 16 January 2019

OCA — Wed, 16 Jan 2019 12:23:54 GMT

←Older revision		Revision as of 12:23, 16 January 2019
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5u8i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5u8i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:30, 15 November 2017

OCA — Wed, 15 Nov 2017 19:30:08 GMT

←Older revision		Revision as of 19:30, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5u8i' size='340' side='right' caption='[[5u8i]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5u8i' size='340' side='right' caption='[[5u8i]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u8i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u8i]] 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=5U8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8I 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">[[5u8h\|5u8h]], [[5u8g\|5u8g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u8h\|5u8h]], [[5u8g\|5u8g]]</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=5u8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8i OCA], [http://pdbe.org/5u8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u8i RCSB], [http://www.ebi.ac.uk/pdbsum/5u8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8i 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=5u8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8i OCA], [http://pdbe.org/5u8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u8i RCSB], [http://www.ebi.ac.uk/pdbsum/5u8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8i ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Doublie, S]]		[[Category: Doublie, S]]
	[[Category: Eckenroth, B E]]		[[Category: Eckenroth, B E]]

OCA at 13:56, 27 April 2017

OCA — Thu, 27 Apr 2017 13:56:16 GMT

←Older revision		Revision as of 13:56, 27 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u8i is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==DNA Polymerase Beta S229L crystallized in PEG 400==
		+	<StructureSection load='5u8i' size='340' side='right' caption='[[5u8i]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5u8i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8I 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">[[5u8h\|5u8h]], [[5u8g\|5u8g]]</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=5u8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8i OCA], [http://pdbe.org/5u8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u8i RCSB], [http://www.ebi.ac.uk/pdbsum/5u8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8i 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 ==
		+	With the formidable growth in the volume of genetic information, it has become essential to identify and characterize mutations in macromolecules not only to predict contributions to disease processes but also to guide the design of therapeutic strategies. While mutations of certain residues have a predictable phenotype based on their chemical nature and known structural position, many types of mutations evade prediction based on current information. Described in this work are the crystal structures of two cancer variants located in the palm domain of DNA polymerase beta (pol beta), S229L and G231D, whose biological phenotype was not readily linked to a predictable structural implication. Structural results demonstrate that the mutations elicit their effect through subtle influences on secondary interactions with a residue neighboring the active site. Residues 229 and 231 are 7.5 and 12.5 A, respectively, from the nearest active site residue, with a beta-strand between them. A residue on this intervening strand, M236, appears to transmit fine structural perturbations to the catalytic metal-coordinating residue D256, affecting its conformational stability.

-	~~Authors:~~ Eckenroth, ~~B.E.~~, ~~Doublie~~, S.	+	Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase beta.,Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL, Sweasy JB, Doublie S Biochemistry. 2017 Apr 21. doi: 10.1021/acs.biochem.6b01287. PMID:28402631<ref>PMID:28402631</ref>

-	~~Description: DNA Polymerase Beta S229L crystallized in PEG 400~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Eckenroth, B.E]]~~	+	<div class="pdbe-citations 5u8i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Doublie, S]]		[[Category: Doublie, S]]
		+	[[Category: Eckenroth, B E]]
		+	[[Category: Dna complex]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Lyase]]
		+	[[Category: Lyase-dna complex]]
		+	[[Category: Transferase]]

OCA at 21:42, 25 January 2017

OCA — Wed, 25 Jan 2017 21:42:26 GMT

←Older revision		Revision as of 21:42, 25 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5u8i is ON HOLD	+	The entry 5u8i is ON HOLD until Paper Publication

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

OCA: Protected "5u8i" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:32:36 GMT

Protected "5u8i" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:32, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u8i is ON HOLD Authors: Eckenroth, B.E., Doublie, S. Description: DNA Polymerase Beta S229L crystallized in PEG 400 [[Category: Unreleased Structu...

OCA — Thu, 22 Dec 2016 20:32:35 GMT

New page: '''Unreleased structure''' The entry 5u8i is ON HOLD Authors: Eckenroth, B.E., Doublie, S. Description: DNA Polymerase Beta S229L crystallized in PEG 400 [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5u8i is ON HOLD

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

Description: DNA Polymerase Beta S229L crystallized in PEG 400
[[Category: Unreleased Structures]]
[[Category: Eckenroth, B.E]]
[[Category: Doublie, S]]