1exn - Revision history

OCA at 10:07, 20 March 2024

2024-03-20T10:07:41Z

←Older revision		Revision as of 10:07, 20 March 2024
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	<StructureSection load='1exn' size='340' side='right'caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1exn' size='340' side='right'caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpt5 Bpt5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1EXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T5 Escherichia virus T5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EXN FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">D15 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=10726 BPT5])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3]~~ </~~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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [https://pdbe.org/1exn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [https://www.ebi.ac.uk/pdbsum/1exn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1exn ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [~~http~~://pdbe.org/1exn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1exn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1exn ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~EXO5_BPT5 EXO5_BPT5]~~] 5'-exonucleolytic ~~degradation of double~~-~~stranded~~ (ds) ~~DNA~~. ~~Can also cleave bifurcated nucleic acids such as~~ flap and pseudo-Y substrates in a ~~structure-specific manner. This requires~~ free 5' single-stranded (ss) ~~ends and cleaves at the ds/ss junction~~. ~~Binds DNA pseudo-Y substrates with a dissociation constant of 5 nM~~.	+	[https://www.uniprot.org/uniprot/FEN_BPT5 FEN_BPT5] Catalyzes both the 5'-exonucleolytic and structure-specific endonucleolytic hydrolysis of DNA branched nucleic acid molecules and probably plays a role in viral genome replication (PubMed:9874768, PubMed:15077103, PubMed:10364212). Active on flap (branched duplex DNA containing a free single-stranded 5'-end), 5'overhangs and pseudo-Y structures (PubMed:9874768, PubMed:15077103, PubMed:10364212). The substrates require a free, single-stranded 5' end, with endonucleolytic hydrolysis occurring at the junction of double- and single-stranded DNA (PubMed:9874768). This function may be used for example to trim such branched molecules generated by Okazaki fragments synthesis during replication.[HAMAP-Rule:MF_04140]<ref>PMID:10364212</ref> <ref>PMID:15077103</ref> <ref>PMID:9874768</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=1exn 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=1exn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been shown to possess endonucleolytic activities. T5 5'-3'-exonuclease shares many similarities with the amino terminal of eubacterial DNA polymerases, although, unlike eubacteria, phages such as T5, T4 and T7 express polymerase and 5'-exonuclease proteins from separate genes. Here we report the 2.5-A crystal structure of the phage T5 5'-exonuclease, which reveals a helical arch for binding DNA. We propose a model consistent with a threading mechanism in which single-stranded DNA could slide through the arch, which is formed by two helices, one containing positively charged, and the other hydrophobic, residues. The active site is at the base of the arch, and contains two metal-binding sites.
-
-	A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.,Ceska TA, Sayers JR, Stier G, Suck D Nature. 1996 Jul 4;382(6586):90-3. PMID:8657312<ref>PMID:8657312</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1exn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]		*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
-	*[[Sand box 211\|Sand box 211]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt5~~]]	+	[[Category: Escherichia virus T5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ceska~~, T A~~]]	+	[[Category: Ceska TA]]
-	[[Category: Sayers~~, J R~~]]	+	[[Category: Sayers JR]]
-	[[Category: Stier, G]]	+	[[Category: Stier G]]
-	[[Category: Suck, D]]	+	[[Category: Suck D]]
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease~~]]	+

OCA at 10:24, 18 November 2020

2020-11-18T10:24:40Z

←Older revision		Revision as of 10:24, 18 November 2020
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	==T5 5'-EXONUCLEASE==		==T5 5'-EXONUCLEASE==
-	<StructureSection load='1exn' size='340' side='right' caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1exn' size='340' side='right'caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt5 Bpt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt5 Bpt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1EXN FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 BPT5])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 BPT5])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://pdbe.org/1exn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1exn ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://pdbe.org/1exn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1exn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	==See Also==		==See Also==
-	*[[Exonuclease\|Exonuclease]]	+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
	*[[Sand box 211\|Sand box 211]]		*[[Sand box 211\|Sand box 211]]
	== References ==		== References ==
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	</StructureSection>		</StructureSection>
	[[Category: Bpt5]]		[[Category: Bpt5]]
		+	[[Category: Large Structures]]
	[[Category: Ceska, T A]]		[[Category: Ceska, T A]]
	[[Category: Sayers, J R]]		[[Category: Sayers, J R]]

OCA at 13:59, 11 April 2018

2018-04-11T13:59:32Z

←Older revision		Revision as of 13:59, 11 April 2018
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	==See Also==		==See Also==
		+	*[[Exonuclease\|Exonuclease]]
	*[[Sand box 211\|Sand box 211]]		*[[Sand box 211\|Sand box 211]]
	== References ==		== References ==

OCA at 07:22, 20 December 2017

2017-12-20T07:22:05Z

←Older revision		Revision as of 07:22, 20 December 2017
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		+
	==T5 5'-EXONUCLEASE==		==T5 5'-EXONUCLEASE==
	<StructureSection load='1exn' size='340' side='right' caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1exn' size='340' side='right' caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 BPT5])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 BPT5])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://pdbe.org/1exn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn 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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://pdbe.org/1exn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1exn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/1exn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/1exn_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>
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	==See Also==		==See Also==
-	*[[~~Exonuclease~~\|~~Exonuclease~~]]	+	*[[Sand box 211\|Sand box 211]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:55, 7 February 2016

2016-02-07T06:55:20Z

←Older revision		Revision as of 06:55, 7 February 2016
Line 18:		Line 18:
	<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=1exn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:55, 9 September 2015

2015-09-09T22:55:21Z

←Older revision		Revision as of 22:55, 9 September 2015
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	<StructureSection load='1exn' size='340' side='right' caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1exn' size='340' side='right' caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t5 Enterobacteria phage t5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt5 Bpt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EXN FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 ~~Enterobacteria phage T5~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 BPT5])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn 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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://pdbe.org/1exn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1exn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t5~~]]	+	[[Category: Bpt5]]
	[[Category: Ceska, T A]]		[[Category: Ceska, T A]]
	[[Category: Sayers, J R]]		[[Category: Sayers, J R]]

OCA at 08:47, 24 December 2014

2014-12-24T08:47:13Z

←Older revision		Revision as of 08:47, 24 December 2014
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	<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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn 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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/EXO5_BPT5 EXO5_BPT5]] 5'-exonucleolytic degradation of double-stranded (ds) DNA. Can also cleave bifurcated nucleic acids such as flap and pseudo-Y substrates in a structure-specific manner. This requires free 5' single-stranded (ss) ends and cleaves at the ds/ss junction. Binds DNA pseudo-Y substrates with a dissociation constant of 5 nM.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 20:27, 22 December 2014

2014-12-22T20:27:00Z

←Older revision		Revision as of 20:27, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t5 Enterobacteria phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EXN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t5 Enterobacteria phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EXN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 Enterobacteria phage T5])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 Enterobacteria phage T5])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn 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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacteria phage t5]]		[[Category: Enterobacteria phage t5]]
-	[[Category: Ceska, T A.]]	+	[[Category: Ceska, T A]]
-	[[Category: Sayers, J R.]]	+	[[Category: Sayers, J R]]
-	[[Category: Stier, G.]]	+	[[Category: Stier, G]]
-	[[Category: Suck, D.]]	+	[[Category: Suck, D]]
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nuclease]]		[[Category: Nuclease]]

OCA at 10:18, 28 September 2014

2014-09-28T10:18:07Z

←Older revision		Revision as of 10:18, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1exn.~~png~~\|~~left~~\|200px]]	+	==T5 5'-EXONUCLEASE==
		+	<StructureSection load='1exn' size='340' side='right' caption='[[1exn]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t5 Enterobacteria phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EXN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 Enterobacteria phage T5])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn 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/ex/1exn_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 ==
		+	THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been shown to possess endonucleolytic activities. T5 5'-3'-exonuclease shares many similarities with the amino terminal of eubacterial DNA polymerases, although, unlike eubacteria, phages such as T5, T4 and T7 express polymerase and 5'-exonuclease proteins from separate genes. Here we report the 2.5-A crystal structure of the phage T5 5'-exonuclease, which reveals a helical arch for binding DNA. We propose a model consistent with a threading mechanism in which single-stranded DNA could slide through the arch, which is formed by two helices, one containing positively charged, and the other hydrophobic, residues. The active site is at the base of the arch, and contains two metal-binding sites.

-	~~{{STRUCTURE_1exn\| PDB=1exn \| SCENE= }}~~	+	A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.,Ceska TA, Sayers JR, Stier G, Suck D Nature. 1996 Jul 4;382(6586):90-3. PMID:8657312<ref>PMID:8657312</ref>

-	~~===T5 5'-EXONUCLEASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8657312}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1exn]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t5 Enterobacteria phage t5]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA].~~	+

	==See Also==		==See Also==
	*[[Exonuclease\|Exonuclease]]		*[[Exonuclease\|Exonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008657312<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t5]]		[[Category: Enterobacteria phage t5]]
	[[Category: Ceska, T A.]]		[[Category: Ceska, T A.]]

OCA at 05:54, 20 October 2012

2012-10-20T05:54:57Z

←Older revision		Revision as of 05:54, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1exn]] is a 2 chain structure ~~of [[Exonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t5 Enterobacteria phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA].	+	[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t5 Enterobacteria phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA].

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