4ebe - Revision history

OCA at 14:57, 14 March 2024

2024-03-14T14:57:19Z

← Older revision		Revision as of 14:57, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ebe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ebe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.1Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4ebe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebe OCA], [https://pdbe.org/4ebe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ebe RCSB], [https://www.ebi.ac.uk/pdbsum/4ebe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ebe 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=4ebe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebe OCA], [https://pdbe.org/4ebe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ebe RCSB], [https://www.ebi.ac.uk/pdbsum/4ebe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ebe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN]] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>		[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol iota) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol iota through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol iota in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol iota inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle (chi), which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol iota. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol iota by preventing the Hoog-steen base-pairing mode normally observed for hpol iota-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

	~~A nucleotide analogue induced gain of function corrects the error-prone nature of human~~ DNA polymerase ~~iota.,Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL J Am Chem Soc. 2012 May 26. PMID:22632140<ref>PMID:22632140</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 4ebe" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:02, 28 September 2022

2022-09-28T07:02:25Z

← Older revision		Revision as of 07:02, 28 September 2022
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	==Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota==		==Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota==
	<StructureSection load='4ebe' size='340' side='right' caption='[[4ebe]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4ebe' size='340' side='right'caption='[[4ebe]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ebe]] is a 3 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=4EBE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4EBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ebe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=~~DTP~~:2-~~DEOXYADENOSINE+~~5-~~TRIPHOSPHATE~~'>~~DTP~~</scene>, <scene name='pdbligand=~~GOL:GLYCEROL'>GOL</scene></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC~~:2~~,3-DIDEOXYCYTIDINE~~-5-~~MONOPHOSPHATE~~'>~~DOC~~</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=4ebe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebe OCA], [https://pdbe.org/4ebe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ebe RCSB], [https://www.ebi.ac.uk/pdbsum/4ebe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ebe ProSAT]</span></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3n\|1t3n]], [[2alz\|2alz]]~~, ~~[[3gv5\|3gv5]], [[3gv7\|3gv7]], [[3gv8\|3gv8]], [[3h40\|3h40]], [[4ebc\|4ebc]], [[4ebd\|4ebd]]~~<~~/td></tr>~~
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">POLI, RAD30B ([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=4ebe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebe OCA], [~~http~~://pdbe.org/4ebe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ebe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ebe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ebe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN]] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>		[[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN]] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~DNA-directed DNA polymerase~~]]		[[Category: Homo sapiens]]
	[[Category: ~~Human~~]]		[[Category: Large Structures]]
	[[Category: Banerjee, S]]		[[Category: Banerjee S]]
	[[Category: Eoff~~, R L~~]]		[[Category: Eoff RL]]
	[[Category: Ketkar, A]]		[[Category: Ketkar A]]
	~~[[Category: Polymerase]]~~
	~~[[Category: Transferase-dna complex~~]]

OCA at 08:01, 15 November 2017

2017-11-15T08:01:22Z

← Older revision		Revision as of 08:01, 15 November 2017
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 4ebe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ebe" style="background-color:#fffaf0;"></div>

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

OCA at 00:24, 5 August 2016

2016-08-05T00:24:44Z

← Older revision		Revision as of 00:24, 5 August 2016
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	==Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota==		==Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota==
	<StructureSection load='4ebe' size='340' side='right' caption='[[4ebe]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4ebe' size='340' side='right' caption='[[4ebe]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ebe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ebe]] is a 3 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=4EBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3n\|1t3n]], [[2alz\|2alz]], [[3gv5\|3gv5]], [[3gv7\|3gv7]], [[3gv8\|3gv8]], [[3h40\|3h40]], [[4ebc\|4ebc]], [[4ebd\|4ebd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3n\|1t3n]], [[2alz\|2alz]], [[3gv5\|3gv5]], [[3gv7\|3gv7]], [[3gv8\|3gv8]], [[3h40\|3h40]], [[4ebc\|4ebc]], [[4ebd\|4ebd]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLI, RAD30B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLI, RAD30B ([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=4ebe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ebe RCSB], [http://www.ebi.ac.uk/pdbsum/4ebe 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=4ebe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebe OCA], [http://pdbe.org/4ebe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ebe RCSB], [http://www.ebi.ac.uk/pdbsum/4ebe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ebe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	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 4ebe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Banerjee, S]]		[[Category: Banerjee, S]]
	[[Category: Eoff, R L]]		[[Category: Eoff, R L]]

OCA at 21:09, 24 December 2014

2014-12-24T21:09:17Z

← Older revision		Revision as of 21:09, 24 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~4ebe~~.~~png~~\|~~left~~\|~~200px~~]]		==Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota==
			<StructureSection load='4ebe' size='340' side='right' caption='[[4ebe]], [[Resolution\|resolution]] 2.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4ebe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EBE FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3n\|1t3n]], [[2alz\|2alz]], [[3gv5\|3gv5]], [[3gv7\|3gv7]], [[3gv8\|3gv8]], [[3h40\|3h40]], [[4ebc\|4ebc]], [[4ebd\|4ebd]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLI, RAD30B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=4ebe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ebe RCSB], [http://www.ebi.ac.uk/pdbsum/4ebe PDBsum]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN]] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol iota) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol iota through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol iota in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol iota inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle (chi), which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol iota. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol iota by preventing the Hoog-steen base-pairing mode normally observed for hpol iota-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

	~~{{STRUCTURE_4ebe\| PDB=4ebe \| SCENE= }}~~		A nucleotide analogue induced gain of function corrects the error-prone nature of human DNA polymerase iota.,Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL J Am Chem Soc. 2012 May 26. PMID:22632140<ref>PMID:22632140</ref>

	~~===Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects~~ the ~~Error-Prone Nature~~ of ~~Human DNA Polymerase Iota===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_22632140}}~~		==See Also==
			*[[DNA polymerase\|DNA polymerase]]
	==~~About this Structure~~==		== References ==
	[[~~4ebe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBE OCA~~].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:022632140<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Banerjee, S.]]		[[Category: Banerjee, S]]
	[[Category: Eoff, R L.]]		[[Category: Eoff, R L]]
	[[Category: Ketkar, A.]]		[[Category: Ketkar, A]]
	[[Category: Polymerase]]		[[Category: Polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 07:24, 11 July 2012

2012-07-11T07:24:35Z

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	[[Image:4ebe.~~jpg~~\|left\|200px]]		[[Image:4ebe.png\|left\|200px]]

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	~~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.~~
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	{{STRUCTURE_4ebe\| PDB=4ebe \| SCENE= }}		{{STRUCTURE_4ebe\| PDB=4ebe \| SCENE= }}

	===Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota===		===Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota===


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OCA at 06:14, 13 June 2012

2012-06-13T06:14:03Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4ebe.jpg|left|200px]]
-The entry 4ebe is ON HOLD  until Paper Publication
+<!--
-Authors: Eoff, R.L., Ketkar, A., Banerjee, S.
+===Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota===
-Description: Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

OCA at 07:15, 6 June 2012

2012-06-06T07:15:18Z

← Older revision		Revision as of 07:15, 6 June 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Eoff, R.L., Ketkar, A., Banerjee, S.		Authors: Eoff, R.L., Ketkar, A., Banerjee, S.

	Description: Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota		Description: Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

OCA at 06:40, 11 April 2012

2012-04-11T06:40:28Z

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	Authors: Eoff, R.L., Ketkar, A., Banerjee, S.		Authors: Eoff, R.L., Ketkar, A., Banerjee, S.

	Description: Conformationally Restrained North-methanocarba-2 -deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota		Description: Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

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

2012-04-04T05:47:24Z

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

← Older revision	Revision as of 05:47, 4 April 2012
(No difference)