4irc - Revision history

OCA at 11:59, 1 March 2024

2024-03-01T11:59:13Z

← Older revision		Revision as of 11:59, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4irc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IRC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4irc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IRC 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></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]] 2.67Å</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></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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [https://pdbe.org/4irc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [https://www.ebi.ac.uk/pdbsum/4irc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4irc 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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [https://pdbe.org/4irc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [https://www.ebi.ac.uk/pdbsum/4irc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4irc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>		[https://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The Y-family DNA polymerase IV or PolIV (Escherichia coli) is the founding member of the DinB family and is known to play an important role in stress-induced mutagenesis. We have determined four crystal structures of this enzyme in its pre-catalytic state in complex with substrate DNA presenting the four possible template nucleotides that are paired with the corresponding incoming nucleotide triphosphates. In all four structures, the Ser42 residue in the active site forms interactions with the base moieties of the incipient Watson-Crick base pair. This residue is located close to the centre of the nascent base pair towards the minor groove. In vitro and in vivo assays show that the fidelity of the PolIV enzyme increases drastically when this Ser residue was mutated to Ala. In addition, the structure of PolIV with the mismatch A:C in the active site shows that the Ser42 residue plays an important role in stabilizing dCTP in a conformation compatible with catalysis. Overall, the structural, biochemical and functional data presented here show that the Ser42 residue is present at a strategic location to stabilize mismatches in the PolIV active site, and thus facilitate the appearance of transition and transversion mutations.

	~~A strategically located serine residue is critical for the mutator activity of~~ DNA polymerase ~~IV from Escherichia coli.,Sharma A, Kottur J, Narayanan N, Nair DT Nucleic Acids Res. 2013 Mar 21. PMID:23525461<ref>PMID:23525461</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 4irc" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:05, 16 November 2022

2022-11-16T21:05:37Z

← Older revision		Revision as of 21:05, 16 November 2022
Line 1:		Line 1:

	==Polymerase-DNA complex==		==Polymerase-DNA complex==
	<StructureSection load='4irc' size='340' side='right' caption='[[4irc]], [[Resolution\|resolution]] 2.67Å' scene=''>		<StructureSection load='4irc' size='340' side='right'caption='[[4irc]], [[Resolution\|resolution]] 2.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4irc]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IRC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4irc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IRC 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~~></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></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ir1\|4ir1]], [[4ir9\|4ir9]], [[4irk\|4irk]]</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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [https://pdbe.org/4irc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [https://www.ebi.ac.uk/pdbsum/4irc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4irc ProSAT]</span></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0231, dinB, dinP, JW0221 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [~~http~~://pdbe.org/4irc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4irc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4irc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>		[https://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4irc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4irc" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~DNA~~-~~directed DNA polymerase~~]]		[[Category: Escherichia coli K-12]]
	[[Category: ~~Ecoli~~]]		[[Category: Large Structures]]
	[[Category: Nair~~, D T~~]]		[[Category: Nair DT]]
	[[Category: Sharma, A]]		[[Category: Sharma A]]
	~~[[Category: Dna polymerase]]~~
	~~[[Category: Transferase-dna complex]]~~
	~~[[Category: Y-family~~]]

OCA at 18:17, 4 August 2016

2016-08-04T18:17:13Z

← Older revision		Revision as of 18:17, 4 August 2016
Line 1:		Line 1:

	==Polymerase-DNA complex==		==Polymerase-DNA complex==
	<StructureSection load='4irc' size='340' side='right' caption='[[4irc]], [[Resolution\|resolution]] 2.67Å' scene=''>		<StructureSection load='4irc' size='340' side='right' caption='[[4irc]], [[Resolution\|resolution]] 2.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4irc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IRC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4irc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IRC 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ir1\|4ir1]], [[4ir9\|4ir9]], [[4irk\|4irk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ir1\|4ir1]], [[4ir9\|4ir9]], [[4irk\|4irk]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0231, dinB, dinP, JW0221 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0231, dinB, dinP, JW0221 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [http://www.ebi.ac.uk/pdbsum/4irc 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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [http://pdbe.org/4irc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [http://www.ebi.ac.uk/pdbsum/4irc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4irc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4irc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: ~~Escherichia coli k-12~~]]		[[Category: Ecoli]]
	[[Category: Nair, D T]]		[[Category: Nair, D T]]
	[[Category: Sharma, A]]		[[Category: Sharma, A]]

OCA at 18:06, 24 December 2014

2014-12-24T18:06:56Z

← Older revision		Revision as of 18:06, 24 December 2014
Line 9:		Line 9:
	<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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [http://www.ebi.ac.uk/pdbsum/4irc 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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [http://www.ebi.ac.uk/pdbsum/4irc PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:30, 21 December 2014

2014-12-21T12:30:39Z

← Older revision		Revision as of 12:30, 21 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_4irc~~\| ~~PDB~~=4irc \| ~~SCENE~~= }}		==Polymerase-DNA complex==
	===~~Polymerase~~-DNA ~~complex~~===		<StructureSection load='4irc' size='340' side='right' caption='[[4irc]], [[Resolution\|resolution]] 2.67Å' scene=''>
	~~{{ABSTRACT_PUBMED_23525461}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4irc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IRC 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></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ir1\|4ir1]], [[4ir9\|4ir9]], [[4irk\|4irk]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0231, dinB, dinP, JW0221 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=4irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4irc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4irc RCSB], [http://www.ebi.ac.uk/pdbsum/4irc PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The Y-family DNA polymerase IV or PolIV (Escherichia coli) is the founding member of the DinB family and is known to play an important role in stress-induced mutagenesis. We have determined four crystal structures of this enzyme in its pre-catalytic state in complex with substrate DNA presenting the four possible template nucleotides that are paired with the corresponding incoming nucleotide triphosphates. In all four structures, the Ser42 residue in the active site forms interactions with the base moieties of the incipient Watson-Crick base pair. This residue is located close to the centre of the nascent base pair towards the minor groove. In vitro and in vivo assays show that the fidelity of the PolIV enzyme increases drastically when this Ser residue was mutated to Ala. In addition, the structure of PolIV with the mismatch A:C in the active site shows that the Ser42 residue plays an important role in stabilizing dCTP in a conformation compatible with catalysis. Overall, the structural, biochemical and functional data presented here show that the Ser42 residue is present at a strategic location to stabilize mismatches in the PolIV active site, and thus facilitate the appearance of transition and transversion mutations.

	~~==Function==~~		A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli.,Sharma A, Kottur J, Narayanan N, Nair DT Nucleic Acids Res. 2013 Mar 21. PMID:23525461<ref>PMID:23525461</ref>
	~~[[http://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI]] Poorly processive, error-prone~~ DNA polymerase ~~involved in untargeted mutagenesis~~. ~~Copies undamaged DNA at stalled replication forks~~, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, ~~which provides the bacterium with flexibility in dealing with environmental stress~~, ~~enhancing long-term survival and evolutionary fitness~~. ~~May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII~~.~~<ref>~~PMID:~~9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref>~~ <ref>PMID:~~12060704~~</ref>

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[4irc]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]~~. ~~Full crystallographic information is available from [http:/~~/~~oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA].~~		</div>

	==~~Reference~~==		==See Also==
	~~<ref group~~=~~"xtra">PMID:023525461</ref>~~<references ~~group="xtra"~~/><~~references~~/>		*[[DNA polymerase\|DNA polymerase]]
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Nair, D T.]]		[[Category: Nair, D T]]
	[[Category: Sharma, A.]]		[[Category: Sharma, A]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]
	[[Category: Y-family]]		[[Category: Y-family]]

OCA at 16:33, 19 June 2013

2013-06-19T16:33:31Z

← Older revision		Revision as of 16:33, 19 June 2013
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	==Reference==		==Reference==
	<references group="xtra"/><references/>		<ref group="xtra">PMID:023525461</ref><references group="xtra"/><references/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]

OCA at 22:47, 10 April 2013

2013-04-10T22:47:43Z

← Older revision		Revision as of 22:47, 10 April 2013
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	~~'''Unreleased structure'''~~		{{STRUCTURE_4irc\| PDB=4irc \| SCENE= }}
			===Polymerase-DNA complex===
			{{ABSTRACT_PUBMED_23525461}}

	~~The entry 4irc~~ is ~~ON HOLD~~ ~~until Paper Publication~~		==Function==
			[[http://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>

	~~Authors~~: ~~Nair, D~~.T.~~, Sharma, A~~.		==About this Structure==
			[[4irc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IRC OCA].

	~~Description~~: ~~Polymerase~~-DNA complex		==Reference==
			<references group="xtra"/><references/>
			[[Category: DNA-directed DNA polymerase]]
			[[Category: Escherichia coli k-12]]
			[[Category: Nair, D T.]]
			[[Category: Sharma, A.]]
			[[Category: Dna polymerase]]
			[[Category: Transferase-dna complex]]
			[[Category: Y-family]]

OCA at 08:13, 27 March 2013

2013-03-27T08:13:28Z

← Older revision		Revision as of 08:13, 27 March 2013
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Nair, D.T., Sharma, A.		Authors: Nair, D.T., Sharma, A.

	Description: Polymerase-DNA complex		Description: Polymerase-DNA complex

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

2013-01-23T11:13:59Z

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

← Older revision	Revision as of 11:13, 23 January 2013
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4irc is ON HOLD Authors: Nair, D.T., Sharma, A. Description: Polymerase-DNA complex

2013-01-23T11:13:58Z

New page: '''Unreleased structure''' The entry 4irc is ON HOLD Authors: Nair, D.T., Sharma, A. Description: Polymerase-DNA complex

New page

'''Unreleased structure'''

The entry 4irc is ON HOLD

Authors: Nair, D.T., Sharma, A.

Description: Polymerase-DNA complex