2bpc - Revision history

OCA at 09:17, 14 February 2024

2024-02-14T09:17:21Z

← Older revision		Revision as of 09:17, 14 February 2024
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	<StructureSection load='2bpc' size='340' side='right'caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2bpc' size='340' side='right'caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BPC FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.8Å</td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~span~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [https://pdbe.org/2bpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [https://www.ebi.ac.uk/pdbsum/2bpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bpc 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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [https://pdbe.org/2bpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [https://www.ebi.ac.uk/pdbsum/2bpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bpc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT]] 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.		[https://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT] 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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bpc ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bpc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.

	Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.,Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J Science. 1994 Jun 24;264(5167):1930-5. PMID:7516581<ref>PMID:7516581</ref>		==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2bpc" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Buffalo rat]]~~
	~~[[Category: DNA-directed DNA polymerase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kraut, J]]		[[Category: Rattus norvegicus]]
	[[Category: Kumar, A]]		[[Category: Kraut J]]
	[[Category: Pelletier, H]]		[[Category: Kumar A]]
	[[Category: Sawaya~~, M R~~]]		[[Category: Pelletier H]]
	[[Category: Wilson~~, S H]]~~		[[Category: Sawaya MR]]
	~~[[Category: Nucleotidyltransferase~~]]		[[Category: Wilson SH]]

OCA at 13:15, 24 November 2021

2021-11-24T13:15:29Z

← Older revision		Revision as of 13:15, 24 November 2021
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	<StructureSection load='2bpc' size='340' side='right'caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2bpc' size='340' side='right'caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2BPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BPC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [~~http~~://pdbe.org/2bpc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2bpc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2bpc 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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [https://pdbe.org/2bpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [https://www.ebi.ac.uk/pdbsum/2bpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bpc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT]] 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.		[[https://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT]] 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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 2bpc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2bpc" style="background-color:#fffaf0;"></div>

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

OCA at 07:53, 19 February 2020

2020-02-19T07:53:12Z

← Older revision		Revision as of 07:53, 19 February 2020
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	==CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM==		==CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM==
	<StructureSection load='2bpc' size='340' side='right' caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2bpc' size='340' side='right'caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BPC FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
			[[Category: Large Structures]]
	[[Category: Kraut, J]]		[[Category: Kraut, J]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]

OCA at 06:11, 16 May 2018

2018-05-16T06:11:24Z

← Older revision		Revision as of 06:11, 16 May 2018
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM==		==CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM==
	<StructureSection load='2bpc' size='340' side='right' caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2bpc' size='340' side='right' caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [http://pdbe.org/2bpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [http://www.ebi.ac.uk/pdbsum/2bpc 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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [http://pdbe.org/2bpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [http://www.ebi.ac.uk/pdbsum/2bpc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bpc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bp/2bpc_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bp/2bpc_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bpc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:41, 11 September 2015

2015-09-11T09:41:09Z

← Older revision		Revision as of 09:41, 11 September 2015
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	<StructureSection load='2bpc' size='340' side='right' caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2bpc' size='340' side='right' caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BPC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [http://www.ebi.ac.uk/pdbsum/2bpc 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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [http://pdbe.org/2bpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [http://www.ebi.ac.uk/pdbsum/2bpc PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT]] 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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	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 2bpc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Buffalo rat]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	~~[[Category: Rattus norvegicus]]~~
	[[Category: Kraut, J]]		[[Category: Kraut, J]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]

OCA at 09:55, 8 January 2015

2015-01-08T09:55:38Z

← Older revision		Revision as of 09:55, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BPC FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [http://www.ebi.ac.uk/pdbsum/2bpc 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=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [http://www.ebi.ac.uk/pdbsum/2bpc PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Kraut, J.]]		[[Category: Kraut, J]]
	[[Category: Kumar, A.]]		[[Category: Kumar, A]]
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R]]
	[[Category: Wilson, S H.]]		[[Category: Wilson, S H]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]

OCA at 09:29, 29 September 2014

2014-09-29T09:29:16Z

← Older revision		Revision as of 09:29, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2bpc~~.~~png~~\|~~left~~\|~~200px~~]]		==CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM==
			<StructureSection load='2bpc' size='340' side='right' caption='[[2bpc]], [[Resolution\|resolution]] 2.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BPC FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
			<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [http://www.ebi.ac.uk/pdbsum/2bpc PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bp/2bpc_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.

	~~{{STRUCTURE_2bpc\| PDB=2bpc \| SCENE= }}~~		Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.,Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J Science. 1994 Jun 24;264(5167):1930-5. PMID:7516581<ref>PMID:7516581</ref>

	~~===CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_7516581}}~~

	~~==About this Structure==~~
	~~[[2bpc]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2BPC OCA].~~

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:007516581<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]

OCA at 17:54, 20 October 2012

2012-10-20T17:54:40Z

← Older revision		Revision as of 17:54, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2bpc]] is a 1 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA].		[[2bpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA].

	==See Also==		==See Also==

OCA: Protected "2bpc" [edit=sysop:move=sysop]

2012-07-27T02:23:08Z

Protected "2bpc" [edit=sysop:move=sysop]

← Older revision	Revision as of 02:23, 27 July 2012
(No difference)

OCA at 02:23, 27 July 2012

2012-07-27T02:23:07Z

← Older revision		Revision as of 02:23, 27 July 2012
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	~~{{Seed}}~~
	[[Image:2bpc.png\|left\|200px]]		[[Image:2bpc.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2bpc", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2bpc\| PDB=2bpc \| SCENE= }}		{{STRUCTURE_2bpc\| PDB=2bpc \| SCENE= }}

	===CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM===		===CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_7516581}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 7516581 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_7516581}}		{{ABSTRACT_PUBMED_7516581}}

	==About this Structure==		==About this Structure==
	~~2BPC~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA].		[[2bpc]] is a 1 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA].

			==See Also==
			*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~7516581~~</ref><references group="xtra"/>		<ref group="xtra">PMID:007516581</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
Line 32:		Line 23:
	[[Category: Wilson, S H.]]		[[Category: Wilson, S H.]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:54:45 2009''~~