4flu - Revision history

OCA at 10:51, 6 November 2024

2024-11-06T10:51:31Z

← Older revision		Revision as of 10:51, 6 November 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DPOL_PYRAY DPOL_PYRAY]		[https://www.uniprot.org/uniprot/DPOL_PYRAY DPOL_PYRAY]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Euryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination between deaminated and natural nucleotide(s) by primer extension assays, electrophoretic mobility shift assays, and X-ray crystallography. Structures of complexes between the protein and DNA duplexes with either a dU or a dH in position +4 were solved at 2.3A and 2.9A resolution, respectively. The PabPolB is found in the editing mode. A new metal binding site has been uncovered below the base-checking cavity where the +4 base is flipped out; it is fully hydrated in an octahedral fashion and helps guide the strongly kinked template strand. Four other crystal structures with each of the canonical bases were also solved in the editing mode, and the presence of three nucleotides in the exonuclease site caused a shift in the coordination state of its metal A from octahedral to tetrahedral. Surprisingly, we find that all canonical bases also enter the base-checking pocket with very small differences in the binding geometry and in the calculated binding free energy compared to deaminated ones. To explain how this can lead to stalling of the replication fork, the full catalytic pathway and its branches must be taken into account, during which the base is checked several times. Our results strongly suggest a switch from elongation to editing modes right after nucleotide insertion when the modified base is at position +5.

			Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.,Gouge J, Ralec C, Henneke G, Delarue M J Mol Biol. 2012 Oct 26;423(3):315-36. doi: 10.1016/j.jmb.2012.07.025. Epub 2012 , Aug 16. PMID:22902479<ref>PMID:22902479</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 4flu" style="background-color:#fffaf0;"></div>

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

OCA at 15:28, 14 March 2024

2024-03-14T15:28:27Z

← Older revision		Revision as of 15:28, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] 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=4FLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FLU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] 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=4FLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FLU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 3.1Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=4flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4flu OCA], [https://pdbe.org/4flu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4flu RCSB], [https://www.ebi.ac.uk/pdbsum/4flu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4flu 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=4flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4flu OCA], [https://pdbe.org/4flu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4flu RCSB], [https://www.ebi.ac.uk/pdbsum/4flu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4flu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DPOL_PYRAY DPOL_PYRAY]		[https://www.uniprot.org/uniprot/DPOL_PYRAY DPOL_PYRAY]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Euryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination between deaminated and natural nucleotide(s) by primer extension assays, electrophoretic mobility shift assays, and X-ray crystallography. Structures of complexes between the protein and DNA duplexes with either a dU or a dH in position +4 were solved at 2.3A and 2.9A resolution, respectively. The PabPolB is found in the editing mode. A new metal binding site has been uncovered below the base-checking cavity where the +4 base is flipped out; it is fully hydrated in an octahedral fashion and helps guide the strongly kinked template strand. Four other crystal structures with each of the canonical bases were also solved in the editing mode, and the presence of three nucleotides in the exonuclease site caused a shift in the coordination state of its metal A from octahedral to tetrahedral. Surprisingly, we find that all canonical bases also enter the base-checking pocket with very small differences in the binding geometry and in the calculated binding free energy compared to deaminated ones. To explain how this can lead to stalling of the replication fork, the full catalytic pathway and its branches must be taken into account, during which the base is checked several times. Our results strongly suggest a switch from elongation to editing modes right after nucleotide insertion when the modified base is at position +5.

	Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.,Gouge J, Ralec C, Henneke G, Delarue M J Mol Biol. 2012 Oct 26;423(3):315-36. doi: 10.1016/j.jmb.2012.07.025. Epub 2012 , Aug 16. PMID:22902479<ref>PMID:22902479</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 4flu" style~~=~~"background-color:#fffaf0;"></div>~~
	=~~= References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:57, 19 October 2022

2022-10-19T19:57:39Z

← Older revision		Revision as of 19:57, 19 October 2022
Line 3:		Line 3:
	<StructureSection load='4flu' size='340' side='right'caption='[[4flu]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4flu' size='340' side='right'caption='[[4flu]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"pyrococcus_abyssi"_erauso_et_al~~.~~_1993 "pyrococcus abyssi" erauso et al~~. ~~1993~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FLU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] 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=4FLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FLU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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">[[4flt\|4flt]], [[4flv\|4flv]], [[4flw\|4flw]], [[4flx\|4flx]], [[4fly\|4fly]], [[4flz\|4flz]], [[4fm0\|4fm0]], [[4fm1\|4fm1]], [[4fm2\|4fm2]]</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=4flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4flu OCA], [https://pdbe.org/4flu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4flu RCSB], [https://www.ebi.ac.uk/pdbsum/4flu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4flu ProSAT]</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=4flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4flu OCA], [~~http~~://pdbe.org/4flu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4flu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4flu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4flu ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/DPOL_PYRAY DPOL_PYRAY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4flu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4flu" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Pyrococcus abyssi erauso et al. 1993]]~~
	~~[[Category: DNA-directed DNA polymerase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Delarue, M~~]]		[[Category: Pyrococcus abyssi]]
	[[Category: ~~Gouge, J~~]]		[[Category: Synthetic construct]]
	[[Category: ~~Dna binding~~]]		[[Category: Delarue M]]
	[[Category: ~~Dna polymerase]]~~		[[Category: Gouge J]]
	~~[[Category: Transferase-dna complex~~]]

OCA at 15:52, 29 January 2020

2020-01-29T15:52:22Z

← Older revision		Revision as of 15:52, 29 January 2020
Line 20:		Line 20:

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

OCA at 08:01, 27 March 2019

2019-03-27T08:01:19Z

← Older revision		Revision as of 08:01, 27 March 2019
Line 1:		Line 1:

	==Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode==		==Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode==
	<StructureSection load='4flu' size='340' side='right' caption='[[4flu]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4flu' size='340' side='right'caption='[[4flu]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FLU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FLU FirstGlance]. <br>
Line 27:		Line 27:
	[[Category: Pyrococcus abyssi erauso et al. 1993]]		[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
			[[Category: Large Structures]]
	[[Category: Delarue, M]]		[[Category: Delarue, M]]
	[[Category: Gouge, J]]		[[Category: Gouge, J]]

OCA at 19:54, 15 December 2016

2016-12-15T19:54:30Z

← Older revision		Revision as of 19:54, 15 December 2016
Line 1:		Line 1:

	==Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode==		==Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode==
	<StructureSection load='4flu' size='340' side='right' caption='[[4flu]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4flu' size='340' side='right' caption='[[4flu]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_abyssi Pyrococcus~~ abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FLU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FLU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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">[[4flt\|4flt]], [[4flv\|4flv]], [[4flw\|4flw]], [[4flx\|4flx]], [[4fly\|4fly]], [[4flz\|4flz]], [[4fm0\|4fm0]], [[4fm1\|4fm1]], [[4fm2\|4fm2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4flt\|4flt]], [[4flv\|4flv]], [[4flw\|4flw]], [[4flx\|4flx]], [[4fly\|4fly]], [[4flz\|4flz]], [[4fm0\|4fm0]], [[4fm1\|4fm1]], [[4fm2\|4fm2]]</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=4flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4flu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4flu RCSB], [http://www.ebi.ac.uk/pdbsum/4flu 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=4flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4flu OCA], [http://pdbe.org/4flu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4flu RCSB], [http://www.ebi.ac.uk/pdbsum/4flu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4flu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 4flu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 23:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	~~[[Category: Pyrococcus abyssi]]~~
	[[Category: Delarue, M]]		[[Category: Delarue, M]]
	[[Category: Gouge, J]]		[[Category: Gouge, J]]

OCA at 17:25, 9 December 2014

2014-12-09T17:25:00Z

← Older revision		Revision as of 17:25, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~4flu~~.~~png~~\|~~left~~\|~~200px~~]]		==Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode==
			<StructureSection load='4flu' size='340' side='right' caption='[[4flu]], [[Resolution\|resolution]] 3.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4flu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FLU FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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">[[4flt\|4flt]], [[4flv\|4flv]], [[4flw\|4flw]], [[4flx\|4flx]], [[4fly\|4fly]], [[4flz\|4flz]], [[4fm0\|4fm0]], [[4fm1\|4fm1]], [[4fm2\|4fm2]]</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=4flu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4flu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4flu RCSB], [http://www.ebi.ac.uk/pdbsum/4flu PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Euryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination between deaminated and natural nucleotide(s) by primer extension assays, electrophoretic mobility shift assays, and X-ray crystallography. Structures of complexes between the protein and DNA duplexes with either a dU or a dH in position +4 were solved at 2.3A and 2.9A resolution, respectively. The PabPolB is found in the editing mode. A new metal binding site has been uncovered below the base-checking cavity where the +4 base is flipped out; it is fully hydrated in an octahedral fashion and helps guide the strongly kinked template strand. Four other crystal structures with each of the canonical bases were also solved in the editing mode, and the presence of three nucleotides in the exonuclease site caused a shift in the coordination state of its metal A from octahedral to tetrahedral. Surprisingly, we find that all canonical bases also enter the base-checking pocket with very small differences in the binding geometry and in the calculated binding free energy compared to deaminated ones. To explain how this can lead to stalling of the replication fork, the full catalytic pathway and its branches must be taken into account, during which the base is checked several times. Our results strongly suggest a switch from elongation to editing modes right after nucleotide insertion when the modified base is at position +5.

	~~{{STRUCTURE_4flu\| PDB=4flu \| SCENE= }}~~		Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.,Gouge J, Ralec C, Henneke G, Delarue M J Mol Biol. 2012 Oct 26;423(3):315-36. doi: 10.1016/j.jmb.2012.07.025. Epub 2012 , Aug 16. PMID:22902479<ref>PMID:22902479</ref>

	~~===Pyrococcus abyssi B family DNA polymerase bound to~~ a ~~dsDNA, in edition mode===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_22902479}}~~		==See Also==
			*[[DNA polymerase\|DNA polymerase]]
	==~~About this Structure~~==		== References ==
	[[~~4flu~~]] ~~is a 3 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA].~~		<references/>
			__TOC__
			</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
	[[Category: Delarue, M.]]		[[Category: Delarue, M]]
	[[Category: Gouge, J.]]		[[Category: Gouge, J]]
	[[Category: Dna binding]]		[[Category: Dna binding]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 06:06, 17 October 2012

2012-10-17T06:06:22Z

← Older revision		Revision as of 06:06, 17 October 2012
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	[[Image:4flu.~~jpg~~\|left\|200px]]		[[Image:4flu.png\|left\|200px]]

	{{STRUCTURE_4flu\| PDB=4flu \| SCENE= }}		{{STRUCTURE_4flu\| PDB=4flu \| SCENE= }}
Line 5:		Line 5:
	===Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode===		===Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode===

			{{ABSTRACT_PUBMED_22902479}}

	==About this Structure==		==About this Structure==

OCA at 05:26, 29 August 2012

2012-08-29T05:26:37Z

← Older revision		Revision as of 05:26, 29 August 2012
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		[[Image:4flu.jpg\|left\|200px]]

	~~The entry~~ 4flu ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4flu\| PDB=4flu \| SCENE= }}

	~~Authors: Gouge~~, ~~J., Delarue, M.~~		===Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode===

	~~Description~~: Pyrococcus abyssi ~~B family~~ DNA polymerase ~~bound to a dsDNA~~, ~~in edition mode~~
			==About this Structure==
			[[4flu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLU OCA].
			[[Category: DNA-directed DNA polymerase]]
			[[Category: Pyrococcus abyssi]]
			[[Category: Delarue, M.]]
			[[Category: Gouge, J.]]
			[[Category: Dna binding]]
			[[Category: Dna polymerase]]
			[[Category: Transferase-dna complex]]

OCA at 07:17, 4 July 2012

2012-07-04T07:17:10Z

← Older revision		Revision as of 07:17, 4 July 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Gouge, J., Delarue, M.		Authors: Gouge, J., Delarue, M.

	Description: Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode		Description: Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode