2d7e - Revision history

OCA at 13:46, 13 March 2024

2024-03-13T13:46:58Z

← Older revision		Revision as of 13:46, 13 March 2024
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	<StructureSection load='2d7e' size='340' side='right'caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2d7e' size='340' side='right'caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~priA (~~[~~https://www.ncbi~~.~~nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=562 "Bacillus coli" Migula 1895])~~</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]] 2.5Å</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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [https://pdbe.org/2d7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [https://www.ebi.ac.uk/pdbsum/2d7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7e 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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [https://pdbe.org/2d7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [https://www.ebi.ac.uk/pdbsum/2d7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>		[https://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d7e ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d7e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes with oligonucleotides and the combination of fluorescence correlation spectroscopy and mutagenesis reveal that the N-terminal domain of PriA possesses a binding pocket for the 3'-terminal nucleotide residue of DNA. The interaction with the deoxyribose 3'-OH is essential for the 3'-terminal recognition. In contrast, the direct interaction with 3'-end nucleobase is unexpected, considering the same affinity for oligonucleotides carrying the four bases at the 3' end. Thus, the N-terminal domain of PriA recognizes the 3'-end base in a base-non-selective manner, in addition to the deoxyribose and 5'-side phosphodiester group, of the 3'-terminal nucleotide to acquire both sufficient affinity and non-selectivity to find all of the stalled replication forks generated during DNA duplication. This unique feature is prerequisite for the proper positioning of the helicase domain of PriA on the unreplicated double-stranded DNA.

	Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.,Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D EMBO J. 2007 May 16;26(10):2584-93. doi: 10.1038/sj.emboj.7601697. Epub 2007 Apr , 26. PMID:17464287<ref>PMID:17464287</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2d7e" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kohda, D]]		[[Category: Kohda D]]
	[[Category: Maenaka, K]]		[[Category: Maenaka K]]
	[[Category: Masai, H]]		[[Category: Masai H]]
	[[Category: Ose, T]]		[[Category: Ose T]]
	[[Category: Sasaki, K]]		[[Category: Sasaki K]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Inter-twined~~]]

OCA at 11:55, 3 February 2021

2021-02-03T11:55:02Z

← Older revision		Revision as of 11:55, 3 February 2021
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	==Crystal structure of N-terminal domain of PriA from E.coli==		==Crystal structure of N-terminal domain of PriA from E.coli==
	<StructureSection load='2d7e' size='340' side='right' caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2d7e' size='340' side='right'caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [~~http~~://pdbe.org/2d7e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d7e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7e 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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [https://pdbe.org/2d7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [https://www.ebi.ac.uk/pdbsum/2d7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>		[[https://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: Kohda, D]]		[[Category: Kohda, D]]
	[[Category: Maenaka, K]]		[[Category: Maenaka, K]]

OCA at 15:41, 27 February 2019

2019-02-27T15:41:35Z

← Older revision		Revision as of 15:41, 27 February 2019
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	PriA~~, a DEXH-type~~ DNA ~~helicase, binds specifically~~ to the 3' end of DNA ~~through its~~ N-terminal domain, ~~and~~ is ~~a candidate sensor protein that recognizes arrested DNA replication forks in bacteria~~. ~~We crystallized an~~ N-terminal ~~fragment~~ of PriA in the ~~absence~~ and the ~~presence~~ of ~~oligonucleotides to elucidate~~ the ~~structural basis~~ for the ~~specific recognition~~ of the ~~3' terminus~~ of DNA.		In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes with oligonucleotides and the combination of fluorescence correlation spectroscopy and mutagenesis reveal that the N-terminal domain of PriA possesses a binding pocket for the 3'-terminal nucleotide residue of DNA. The interaction with the deoxyribose 3'-OH is essential for the 3'-terminal recognition. In contrast, the direct interaction with 3'-end nucleobase is unexpected, considering the same affinity for oligonucleotides carrying the four bases at the 3' end. Thus, the N-terminal domain of PriA recognizes the 3'-end base in a base-non-selective manner, in addition to the deoxyribose and 5'-side phosphodiester group, of the 3'-terminal nucleotide to acquire both sufficient affinity and non-selectivity to find all of the stalled replication forks generated during DNA duplication. This unique feature is prerequisite for the proper positioning of the helicase domain of PriA on the unreplicated double-stranded DNA.

	~~Crystallization and preliminary crystallographic analysis~~ of the N-~~terminal domain~~ of PriA ~~from Escherichia coli~~.,Sasaki K, Ose T, ~~Tanaka T~~, ~~Mizukoshi T~~, ~~Ishigaki~~ T~~, Maenaka K~~, Masai H, Kohda D ~~Biochim Biophys Acta~~. ~~2006 Jan~~;~~1764~~(1):~~157~~-60. Epub ~~2005 Oct 3~~. PMID:~~16226927~~<ref>PMID:~~16226927~~</ref>		Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.,Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D EMBO J. 2007 May 16;26(10):2584-93. doi: 10.1038/sj.emboj.7601697. Epub 2007 Apr , 26. PMID:17464287<ref>PMID:17464287</ref>

	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>

OCA at 06:25, 30 May 2018

2018-05-30T06:25:22Z

← Older revision		Revision as of 06:25, 30 May 2018
Line 1:		Line 1:

	==Crystal structure of N-terminal domain of PriA from E.coli==		==Crystal structure of N-terminal domain of PriA from E.coli==
	<StructureSection load='2d7e' size='340' side='right' caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2d7e' size='340' side='right' caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [http://pdbe.org/2d7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [http://www.ebi.ac.uk/pdbsum/2d7e 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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [http://pdbe.org/2d7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [http://www.ebi.ac.uk/pdbsum/2d7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d7e_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d7e_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 21:43, 8 February 2016

2016-02-08T21:43:27Z

← Older revision		Revision as of 21:43, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d7e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:39, 10 September 2015

2015-09-10T15:39:41Z

← Older revision		Revision as of 15:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2d7e' size='340' side='right' caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2d7e' size='340' side='right' caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [http://www.ebi.ac.uk/pdbsum/2d7e 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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [http://pdbe.org/2d7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [http://www.ebi.ac.uk/pdbsum/2d7e PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 2d7e" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Kohda, D]]		[[Category: Kohda, D]]
	[[Category: Maenaka, K]]		[[Category: Maenaka, K]]

OCA at 02:20, 25 December 2014

2014-12-25T02:20:19Z

← Older revision		Revision as of 02:20, 25 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [http://www.ebi.ac.uk/pdbsum/2d7e 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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [http://www.ebi.ac.uk/pdbsum/2d7e PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Kohda, D.]]		[[Category: Kohda, D]]
	[[Category: Maenaka, K.]]		[[Category: Maenaka, K]]
	[[Category: Masai, H.]]		[[Category: Masai, H]]
	[[Category: Ose, T.]]		[[Category: Ose, T]]
	[[Category: Sasaki, K.]]		[[Category: Sasaki, K]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Inter-twined]]		[[Category: Inter-twined]]

OCA at 09:50, 29 September 2014

2014-09-29T09:50:06Z

← Older revision		Revision as of 09:50, 29 September 2014
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	[[Image:~~2d7e~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of N-terminal domain of PriA from E.coli==
			<StructureSection load='2d7e' size='340' side='right' caption='[[2d7e]], [[Resolution\|resolution]] 2.50Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [http://www.ebi.ac.uk/pdbsum/2d7e PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d7e_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			PriA, a DEXH-type DNA helicase, binds specifically to the 3' end of DNA through its N-terminal domain, and is a candidate sensor protein that recognizes arrested DNA replication forks in bacteria. We crystallized an N-terminal fragment of PriA in the absence and the presence of oligonucleotides to elucidate the structural basis for the specific recognition of the 3' terminus of DNA.

	~~{{STRUCTURE_2d7e\| PDB=2d7e \| SCENE= }}~~		Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli.,Sasaki K, Ose T, Tanaka T, Mizukoshi T, Ishigaki T, Maenaka K, Masai H, Kohda D Biochim Biophys Acta. 2006 Jan;1764(1):157-60. Epub 2005 Oct 3. PMID:16226927<ref>PMID:16226927</ref>

	~~===Crystal structure~~ of ~~N-terminal domain~~ of ~~PriA from E~~.~~coli===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16226927}}~~

	~~==About this Structure==~~
	~~[[2d7e]] is a 4 chain structure with sequence from [http:/~~/~~en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA].~~

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016226927<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Kohda, D.]]		[[Category: Kohda, D.]]

OCA at 11:34, 20 October 2012

2012-10-20T11:34:26Z

← Older revision		Revision as of 11:34, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2d7e]] is a 4 chain structure ~~of [[Helicase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA].		[[2d7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA].

	==See Also==		==See Also==

OCA: Protected "2d7e" [edit=sysop:move=sysop]

2012-07-26T05:49:45Z

Protected "2d7e" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:49, 26 July 2012
(No difference)