4e0d - Revision history

OCA at 14:49, 14 March 2024

2024-03-14T14:49:04Z

← Older revision		Revision as of 14:49, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e0d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426] 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E0D FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e0d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426] 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E0D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.58Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [https://pdbe.org/4e0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [https://www.ebi.ac.uk/pdbsum/4e0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e0d 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=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [https://pdbe.org/4e0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [https://www.ebi.ac.uk/pdbsum/4e0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e0d 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 4e0d" style~~=~~"background-color:#fffaf0;"></div>~~
	~~== References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:42, 28 September 2022

2022-09-28T06:42:55Z

← Older revision		Revision as of 06:42, 28 September 2022
Line 1:		Line 1:

	==Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA==		==Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA==
	<StructureSection load='4e0d' size='340' side='right' caption='[[4e0d]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='4e0d' size='340' side='right'caption='[[4e0d]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e0d]] is a 3 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E0D FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e0d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426] 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E0D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [https://pdbe.org/4e0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [https://www.ebi.ac.uk/pdbsum/4e0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e0d 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]], [[4dqp\|4dqp]], [[4dqi\|4dqi]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2730, GYMC61_0787, polA ([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=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [~~http~~://pdbe.org/4e0d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e0d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e0d 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 4e0d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4e0d" 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: Synthetic construct]]
	[[Category: ~~Wang, W~~]]		[[Category: Beese LS]]
	[[Category: ~~Dna polymerase i]]~~		[[Category: Wang W]]
	~~[[Category: Protein-dna complex]]~~
	~~[[Category: Transferase-dna complex~~]]

OCA at 20:25, 11 August 2016

2016-08-11T20:25:15Z

← Older revision		Revision as of 20:25, 11 August 2016
Line 1:		Line 1:

	==Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA==		==Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA==
	<StructureSection load='4e0d' size='340' side='right' caption='[[4e0d]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='4e0d' size='340' side='right' caption='[[4e0d]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e0d]] is a 3 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E0D FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e0d]] is a 3 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E0D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]], [[4dqp\|4dqp]], [[4dqi\|4dqi]]</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]], [[4dqp\|4dqp]], [[4dqi\|4dqi]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2730, GYMC61_0787, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1462 Geobacillus kaustophilus~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2730, GYMC61_0787, polA ([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=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [http://www.ebi.ac.uk/pdbsum/4e0d 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=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [http://pdbe.org/4e0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [http://www.ebi.ac.uk/pdbsum/4e0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e0d 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 4e0d" 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~~]]		[[Category: Geoka]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Wang, W]]		[[Category: Wang, W]]

OCA at 13:25, 4 January 2015

2015-01-04T13:25:59Z

OCA at 06:54, 25 June 2014

2014-06-25T06:54:08Z

← Older revision		Revision as of 06:54, 25 June 2014
Line 1:		Line 1:
	[[~~Image~~:~~4e0d~~.~~png~~\|~~left~~\|~~200px~~]]		==Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA==
			<StructureSection load='4e0d' size='340' side='right' caption='[[4e0d]], [[Resolution\|resolution]] 1.58Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e0d]] is a 3 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E0D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><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><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]], [[4dqp\|4dqp]], [[4dqi\|4dqi]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2730, GYMC61_0787, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [http://www.ebi.ac.uk/pdbsum/4e0d 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_4e0d\| PDB=4e0d \| 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>

	~~===Binary complex~~ of ~~Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA===~~		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 ==
	[[~~4e0d]~~] is a 3 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=4E0D OCA].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:022648417<~~/~~ref~~><~~ref group="xtra">PMID:022006298</ref><references group="xtra"~~/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]

OCA at 05:50, 5 September 2012

2012-09-05T05:50:08Z

← Older revision		Revision as of 05:50, 5 September 2012
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	[[Image:4e0d.png\|left\|200px]]		[[Image:4e0d.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_4e0d", 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.~~
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	{{STRUCTURE_4e0d\| PDB=4e0d \| SCENE= }}		{{STRUCTURE_4e0d\| PDB=4e0d \| SCENE= }}

	===Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA===		===Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22648417}}, adds the Publication Abstract to the page~~
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	{{ABSTRACT_PUBMED_22648417}}		{{ABSTRACT_PUBMED_22648417}}

OCA at 05:22, 13 June 2012

2012-06-13T05:22:33Z

← Older revision		Revision as of 05:22, 13 June 2012
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	[[Image:4e0d.~~jpg~~\|left\|200px]]		[[Image:4e0d.png\|left\|200px]]

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	The line below this paragraph, {{~~ABSTRACT_PUBMED_22006298~~}}, adds the Publication Abstract to the page		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 ~~22006298~~ is the PubMed ID number.		(as it appears on PubMed at http://www.pubmed.gov), where 22648417 is the PubMed ID number.
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	{{~~ABSTRACT_PUBMED_22006298~~}}		{{ABSTRACT_PUBMED_22648417}}

	==About this Structure==		==About this Structure==
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	==Reference==		==Reference==
	<ref group="xtra">PMID:022006298</ref><references group="xtra"/>		<ref group="xtra">PMID:022648417</ref><ref group="xtra">PMID:022006298</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]

OCA at 07:55, 6 June 2012

2012-06-06T07:55:17Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4e0d.jpg|left|200px]]
-The entry 4e0d is ON HOLD  until Paper Publication
+<!--
-Authors: Wang, W., Beese, L.S.
+===Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA===
-Description: Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA

OCA at 08:45, 16 May 2012

2012-05-16T08:45:49Z

← Older revision		Revision as of 08:45, 16 May 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e0d is ON HOLD		The entry 4e0d is ON HOLD until Paper Publication

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

	Description: Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA		Description: Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA

OCA: Protected "4e0d" [edit=sysop:move=sysop]

2012-03-14T06:14:49Z

Protected "4e0d" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:14, 14 March 2012
(No difference)

← Older revision		Revision as of 13:25, 4 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e0d]] is a 3 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E0D FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e0d]] is a 3 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=4E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E0D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><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><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]], [[4dqp\|4dqp]], [[4dqi\|4dqi]]</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]], [[4dqp\|4dqp]], [[4dqi\|4dqi]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2730, GYMC61_0787, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2730, GYMC61_0787, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [http://www.ebi.ac.uk/pdbsum/4e0d 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=4e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e0d RCSB], [http://www.ebi.ac.uk/pdbsum/4e0d PDBsum]</span></td></tr>
	<table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 27:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus kaustophilus]]		[[Category: Geobacillus kaustophilus]]
	[[Category: Beese, L S.]]		[[Category: Beese, L S]]
	[[Category: Wang, W.]]		[[Category: Wang, W]]
	[[Category: Dna polymerase i]]		[[Category: Dna polymerase i]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]