4pha - Revision history

OCA at 00:43, 28 December 2023

2023-12-28T00:43:53Z

← Older revision		Revision as of 00:43, 28 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pha]] 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=4PHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pha]] 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=4PHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PHA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.52Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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'>[https://proteopedia.org/fgij/fg.htm?mol=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [https://pdbe.org/4pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [https://www.ebi.ac.uk/pdbsum/4pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pha 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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [https://pdbe.org/4pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [https://www.ebi.ac.uk/pdbsum/4pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pha ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4pha" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4pha" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:02, 1 February 2023

2023-02-01T13:02:44Z

← Older revision		Revision as of 13:02, 1 February 2023
Line 3:		Line 3:
	<StructureSection load='4pha' size='340' side='right'caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='4pha' size='340' side='right'caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pha]] 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=4PHA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pha]] 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=4PHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PHA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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'>[https://proteopedia.org/fgij/fg.htm?mol=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [https://pdbe.org/4pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [https://www.ebi.ac.uk/pdbsum/4pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pha 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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [~~http~~://pdbe.org/4pha PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4pha PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4pha 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 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4pha" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4pha" 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: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Koag, M C~~]]		[[Category: Synthetic construct]]
	[[Category: ~~Lee, S~~]]		[[Category: Koag MC]]
	[[Category: ~~Human dna polymerase beta]]~~		[[Category: Lee S]]
	~~[[Category: Lyase-dna complex]]~~
	~~[[Category: Transferase~~]]

OCA at 12:13, 17 July 2019

2019-07-17T12:13:57Z

← Older revision		Revision as of 12:13, 17 July 2019
Line 1:		Line 1:

	==Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP==		==Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP==
	<StructureSection load='4pha' size='340' side='right' caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='4pha' size='340' side='right'caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pha]] 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=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pha]] 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=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4pha" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4pha" 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: Koag, M C]]		[[Category: Koag, M C]]
	[[Category: Lee, S]]		[[Category: Lee, S]]

OCA at 14:52, 15 November 2017

2017-11-15T14:52:32Z

← Older revision		Revision as of 14:52, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='4pha' size='340' side='right' caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='4pha' size='340' side='right' caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pha]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pha]] 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=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://pdbe.org/4pha PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pha 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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://pdbe.org/4pha PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pha ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4pha" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4pha" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
	[[Category: Koag, M C]]		[[Category: Koag, M C]]
	[[Category: Lee, S]]		[[Category: Lee, S]]
	[[Category: Human dna polymerase beta]]		[[Category: Human dna polymerase beta]]
			[[Category: Lyase-dna complex]]
			[[Category: Transferase]]

OCA at 07:47, 5 August 2016

2016-08-05T07:47:58Z

← Older revision		Revision as of 07:47, 5 August 2016
Line 1:		Line 1:

	==Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP==		==Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP==
	<StructureSection load='4pha' size='340' side='right' caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='4pha' size='340' side='right' caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4pha]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pha]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha 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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://pdbe.org/4pha PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pha ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4pha" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:25, 25 December 2014

2014-12-25T00:25:42Z

← Older revision		Revision as of 00:25, 25 December 2014
Line 6:		Line 6:
	<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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha 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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha PDBsum]</span></td></tr>
	</table>		</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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Koag, M C.]]		[[Category: Koag, M C]]
	[[Category: Lee, S.]]		[[Category: Lee, S]]
	[[Category: Human dna polymerase beta]]		[[Category: Human dna polymerase beta]]

OCA at 05:52, 8 October 2014

2014-10-08T05:52:01Z

← Older revision		Revision as of 05:52, 8 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pha]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pha]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha 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=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha PDBsum]</span></td></tr>
	<table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:35, 24 September 2014

2014-09-24T10:35:29Z

← Older revision		Revision as of 10:35, 24 September 2014
Line 1:		Line 1:
	'''~~Unreleased~~ structure'''		==Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP==
			<StructureSection load='4pha' size='340' side='right' caption='[[4pha]], [[Resolution\|resolution]] 2.52Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4pha]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHA FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pha RCSB], [http://www.ebi.ac.uk/pdbsum/4pha PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta (polbeta), we report four crystal structures of polbeta complexed with dGdTTP and dAdCTP mismatches in the presence of Mg2+ or Mn2+. The Mg2+-bound ground-state structures show that the dAdCTP-Mg2+ complex adopts an 'intermediate' protein conformation while the dGdTTP-Mg2+ complex adopts an open protein conformation. The Mn2+-bound 'pre-chemistry-state' structures show that the dAdCTP-Mn2+ complex is structurally very similar to the dAdCTP-Mg2+ complex, whereas the dGdTTP-Mn2+ complex undergoes a large-scale conformational change to adopt a Watson-Crick-like dGdTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that polbeta increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, polbeta appears to allow only a Watson-Crick-like conformation for purine*pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson-Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of polbeta.

	The ~~entry 4pha is ON HOLD until Paper Publication~~		The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta,Koag MC, Nam K, Lee S Nucleic Acids Res. 2014 Sep 8. pii: gku789. PMID:25200079<ref>PMID:25200079</ref>

	~~Authors~~: Koag, M.C., Lee, S.		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~Description~~: ~~Structure of human DNA~~ polymerase beta ~~complexed with A in the template base paired with incoming non-hydrolyzable CTP~~		== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Koag, M C.]]
			[[Category: Lee, S.]]
			[[Category: Human dna polymerase beta]]

OCA at 09:40, 16 July 2014

2014-07-16T09:40:53Z

← Older revision		Revision as of 09:40, 16 July 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4pha is ON HOLD		The entry 4pha is ON HOLD until Paper Publication

	Authors: ~~Lee, S,~~ Koag, M.C		Authors: Koag, M.C., Lee, S.

	Description: Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP		Description: Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP

OCA: Protected "4pha" [edit=sysop:move=sysop]

2014-05-14T07:08:12Z

Protected "4pha" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:08, 14 May 2014
(No difference)