4dqp - Revision history

OCA at 14:42, 14 March 2024

OCA — Thu, 14 Mar 2024 14:42:33 GMT

←Older revision		Revision as of 14:42, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dqp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DQP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dqp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DQP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.74Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dqp OCA], [https://pdbe.org/4dqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dqp RCSB], [https://www.ebi.ac.uk/pdbsum/4dqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dqp 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=4dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dqp OCA], [https://pdbe.org/4dqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dqp RCSB], [https://www.ebi.ac.uk/pdbsum/4dqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dqp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]]	+	[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	In addition to discriminating against base-pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxy nucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2' hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present ten high-resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment (BF) variants complexed with deoxy-, ribo-, dideoxy-nucleotides, and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites, and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base-pair discrimination.	+

-	Structural factors that determine selectivity of a high-fidelity DNA polymerase for deoxy-, dideoxy-, and ribo-nucleotides.,Wang W, Wu EY, Hellinga HW, Beese LS J Biol Chem. 2012 May 30. PMID:22648417<ref>PMID:22648417</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 4dqp" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:34, 21 September 2022

OCA — Wed, 21 Sep 2022 08:34:38 GMT

←Older revision		Revision as of 08:34, 21 September 2022
Line 1:		Line 1:

	==Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)==		==Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)==
-	<StructureSection load='4dqp' size='340' side='right' caption='[[4dqp]], [[Resolution\|resolution]] 1.74Å' scene=''>	+	<StructureSection load='4dqp' size='340' side='right'caption='[[4dqp]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dqp]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Geoka Geoka~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dqp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DQP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dqp OCA], [https://pdbe.org/4dqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dqp RCSB], [https://www.ebi.ac.uk/pdbsum/4dqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dqp ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[4dqq\|4dqq]], [[4dqr\|4dqr]], [[4dqs\|4dqs]], [[4ds4\|4ds4]], [[4ds5\|4ds5]], [[4dse\|4dse]], [[4dsf\|4dsf]], [[4diq\|4diq]], [[4e0d\|4e0d]]</td></tr>~~	+
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</~~b></td><td class="sblockDat"~~>~~polA~~, ~~GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])~~<~~/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=4dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dqp OCA], [~~http~~://pdbe.org/4dqp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dqp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dqp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dqp ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4dqp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4dqp" 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: Geobacillus kaustophilus HTA426]]
-	[[Category: ~~Geoka~~]]	+	[[Category: Large Structures]]
-	[[Category: Beese~~, L S~~]]	+	[[Category: Beese LS]]
-	[[Category: Wang, W]]	+	[[Category: Wang W]]
-	~~[[Category: Cytosine-guanine]]~~	+
-	~~[[Category: Dna polymerase i]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 16:30, 11 August 2016

OCA — Thu, 11 Aug 2016 16:30:15 GMT

←Older revision		Revision as of 16:30, 11 August 2016
Line 1:		Line 1:
		+
	==Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)==		==Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)==
	<StructureSection load='4dqp' size='340' side='right' caption='[[4dqp]], [[Resolution\|resolution]] 1.74Å' scene=''>		<StructureSection load='4dqp' size='340' side='right' caption='[[4dqp]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DQP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[4dqq\|4dqq]], [[4dqr\|4dqr]], [[4dqs\|4dqs]], [[4ds4\|4ds4]], [[4ds5\|4ds5]], [[4dse\|4dse]], [[4dsf\|4dsf]], [[4diq\|4diq]], [[4e0d\|4e0d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dqq\|4dqq]], [[4dqr\|4dqr]], [[4dqs\|4dqs]], [[4ds4\|4ds4]], [[4ds5\|4ds5]], [[4dse\|4dse]], [[4dsf\|4dsf]], [[4diq\|4diq]], [[4e0d\|4e0d]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 ~~Geobacillus kaustophilus HTA426~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</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=4dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dqp RCSB], [http://www.ebi.ac.uk/pdbsum/4dqp 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=4dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dqp OCA], [http://pdbe.org/4dqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dqp RCSB], [http://www.ebi.ac.uk/pdbsum/4dqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dqp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	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 4dqp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: ~~Geobacillus kaustophilus hta426~~]]	+	[[Category: Geoka]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Wang, W]]		[[Category: Wang, W]]

OCA at 13:08, 4 January 2015

OCA — Sun, 04 Jan 2015 13:08:39 GMT

←Older revision		Revision as of 13:08, 4 January 2015
Line 1:		Line 1:
-	[[~~Image:~~4dqp.~~png~~\|~~left~~\|~~200px~~]]	+	==Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)==
		+	<StructureSection load='4dqp' size='340' side='right' caption='[[4dqp]], [[Resolution\|resolution]] 1.74Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DQP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[4dqq\|4dqq]], [[4dqr\|4dqr]], [[4dqs\|4dqs]], [[4ds4\|4ds4]], [[4ds5\|4ds5]], [[4dse\|4dse]], [[4dsf\|4dsf]], [[4diq\|4diq]], [[4e0d\|4e0d]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 Geobacillus kaustophilus HTA426])</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=4dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dqp RCSB], [http://www.ebi.ac.uk/pdbsum/4dqp PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In addition to discriminating against base-pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxy nucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2' hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present ten high-resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment (BF) variants complexed with deoxy-, ribo-, dideoxy-nucleotides, and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites, and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base-pair discrimination.

-	~~{{STRUCTURE_4dqp\| PDB=4dqp \| SCENE= }}~~	+	Structural factors that determine selectivity of a high-fidelity DNA polymerase for deoxy-, dideoxy-, and ribo-nucleotides.,Wang W, Wu EY, Hellinga HW, Beese LS J Biol Chem. 2012 May 30. PMID:22648417<ref>PMID:22648417</ref>

-	~~===Ternary complex~~ of ~~Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG~~ of ~~template)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22648417}}~~	+	==See Also==
-		+	*[[DNA polymerase\|DNA polymerase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4dqp~~]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:022648417<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus hta426]]		[[Category: Geobacillus kaustophilus hta426]]
-	[[Category: Beese, L S.]]	+	[[Category: Beese, L S]]
-	[[Category: Wang, W.]]	+	[[Category: Wang, W]]
	[[Category: Cytosine-guanine]]		[[Category: Cytosine-guanine]]
	[[Category: Dna polymerase i]]		[[Category: Dna polymerase i]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 09:54, 21 November 2012

OCA — Wed, 21 Nov 2012 09:54:54 GMT

←Older revision		Revision as of 09:54, 21 November 2012
Line 1:		Line 1:
	[[Image:4dqp.png\|left\|200px]]		[[Image:4dqp.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_4dqp", 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_4dqp\| PDB=4dqp \| SCENE= }}		{{STRUCTURE_4dqp\| PDB=4dqp \| SCENE= }}

	===Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)===		===Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22648417}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22648417 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22648417}}		{{ABSTRACT_PUBMED_22648417}}

	==About this Structure==		==About this Structure==
-	[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_kaustophilus~~ Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA].	+	[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:022648417</ref><references group="xtra"/>		<ref group="xtra">PMID:022648417</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Geobacillus kaustophilus]]	+	[[Category: Geobacillus kaustophilus hta426]]
	[[Category: Beese, L S.]]		[[Category: Beese, L S.]]
	[[Category: Wang, W.]]		[[Category: Wang, W.]]

OCA at 05:23, 13 June 2012

OCA — Wed, 13 Jun 2012 05:23:32 GMT

←Older revision		Revision as of 05:23, 13 June 2012
Line 1:		Line 1:
-	[[Image:4dqp.~~jpg~~\|left\|200px]]	+	[[Image:4dqp.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)===		===Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22648417}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22648417 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22648417}}

	==About this Structure==		==About this Structure==
	[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA].		[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022648417</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]

OCA at 07:54, 6 June 2012

OCA — Wed, 06 Jun 2012 07:54:10 GMT

←Older revision		Revision as of 07:54, 6 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4dqp.jpg\|left\|200px]]

-	The ~~entry 4dqp~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4dqp", 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_4dqp\| PDB=4dqp \| SCENE= }}

-	~~Authors: Wang~~, W., ~~Beese, L.S.~~	+	===Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)===

-	~~Description~~: ~~Ternary complex of Bacillus~~ DNA ~~Polymerase I Large Fragment,~~ DNA ~~duplex~~, ~~and ddCTP (paired with dG of template)~~	+
		+	==About this Structure==
		+	[[4dqp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DQP OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Geobacillus kaustophilus]]
		+	[[Category: Beese, L S.]]
		+	[[Category: Wang, W.]]
		+	[[Category: Cytosine-guanine]]
		+	[[Category: Dna polymerase i]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Transferase-dna complex]]

OCA at 18:52, 2 May 2012

OCA — Wed, 02 May 2012 18:52:05 GMT

←Older revision		Revision as of 18:52, 2 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dqp is ON HOLD	+	The entry 4dqp is ON HOLD until Paper Publication

	Authors: Wang, W., Beese, L.S.		Authors: Wang, W., Beese, L.S.

	Description: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)		Description: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)

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

OCA — Wed, 22 Feb 2012 07:33:25 GMT

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

←Older revision

Revision as of 07:33, 22 February 2012

OCA: New page: '''Unreleased structure''' The entry 4dqp is ON HOLD Authors: Wang, W., Beese, L.S. Description: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (pai...

OCA — Wed, 22 Feb 2012 07:33:24 GMT

New page: '''Unreleased structure''' The entry 4dqp is ON HOLD Authors: Wang, W., Beese, L.S. Description: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (pai...

New page

'''Unreleased structure'''

The entry 4dqp is ON HOLD

Authors: Wang, W., Beese, L.S.

Description: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)