2yv0 - Revision history

OCA at 09:05, 25 October 2023

OCA — Wed, 25 Oct 2023 09:05:22 GMT

←Older revision		Revision as of 09:05, 25 October 2023
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	<StructureSection load='2yv0' size='340' side='right'caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='2yv0' size='340' side='right'caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rnhA ([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]] 1.4Å</td></tr>
-	~~<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'~~>[~~https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.~~1~~.26~~.4 ~~3.1.26.4] </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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [https://pdbe.org/2yv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [https://www.ebi.ac.uk/pdbsum/2yv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yv0 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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [https://pdbe.org/2yv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [https://www.ebi.ac.uk/pdbsum/2yv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yv0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]	+	[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonuclease H]]~~	+	[[Category: Haruki M]]
-	[[Category: Haruki, M]]	+	[[Category: Kanaya S]]
-	[[Category: Kanaya, S]]	+	[[Category: Koga Y]]
-	[[Category: Koga, Y]]	+	[[Category: Motegi T]]
-	[[Category: Motegi, T]]	+	[[Category: Tadokoro T]]
-	[[Category: Tadokoro, T]]	+	[[Category: Takano K]]
-	[[Category: Takano, K]]	+
-	~~[[Category: E. coli]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Quintuple thermostabilizing mutation]]~~	+
-	~~[[Category: Rnase hi~~]]	+

OCA at 07:10, 10 November 2021

OCA — Wed, 10 Nov 2021 07:10:30 GMT

←Older revision		Revision as of 07:10, 10 November 2021
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	==Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations==		==Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations==
-	<StructureSection load='2yv0' size='340' side='right' caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='2yv0' size='340' side='right'caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA ([~~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">rnhA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [~~http~~://pdbe.org/2yv0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2yv0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2yv0 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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [https://pdbe.org/2yv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [https://www.ebi.ac.uk/pdbsum/2yv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yv0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]	+	[[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	*[[Temp\|Temp]]	+
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Haruki, M]]		[[Category: Haruki, M]]

OCA at 08:52, 17 October 2018

OCA — Wed, 17 Oct 2018 08:52:58 GMT

←Older revision		Revision as of 08:52, 17 October 2018
Line 1:		Line 1:
		+
	==Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations==		==Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations==
	<StructureSection load='2yv0' size='340' side='right' caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='2yv0' size='340' side='right' caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>
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	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA ([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">rnhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [http://pdbe.org/2yv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yv0 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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [http://pdbe.org/2yv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yv0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yv0 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/yv/2yv0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yv/2yv0_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 21:41, 9 February 2016

OCA — Tue, 09 Feb 2016 21:41:10 GMT

←Older revision		Revision as of 21:41, 9 February 2016
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	<StructureSection load='2yv0' size='340' side='right' caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='2yv0' size='340' side='right' caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA ([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">rnhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yv0 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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [http://pdbe.org/2yv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yv0 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<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=2yv0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 2yv0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
-	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Haruki, M]]		[[Category: Haruki, M]]

OCA at 09:43, 25 December 2014

OCA — Thu, 25 Dec 2014 09:43:31 GMT

←Older revision		Revision as of 09:43, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA ([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">rnhA ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yv0 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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yv0 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
		+	*[[Temp\|Temp]]
		+	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 38:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
-	[[Category: Haruki, M.]]	+	[[Category: Haruki, M]]
-	[[Category: Kanaya, S.]]	+	[[Category: Kanaya, S]]
-	[[Category: Koga, Y.]]	+	[[Category: Koga, Y]]
-	[[Category: Motegi, T.]]	+	[[Category: Motegi, T]]
-	[[Category: Tadokoro, T.]]	+	[[Category: Tadokoro, T]]
-	[[Category: Takano, K.]]	+	[[Category: Takano, K]]
	[[Category: E. coli]]		[[Category: E. coli]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Quintuple thermostabilizing mutation]]		[[Category: Quintuple thermostabilizing mutation]]
	[[Category: Rnase hi]]		[[Category: Rnase hi]]

OCA at 05:18, 2 October 2014

OCA — Thu, 02 Oct 2014 05:18:36 GMT

←Older revision		Revision as of 05:18, 2 October 2014
Line 1:		Line 1:
-	[[~~Image~~:2yv0.~~png\|left~~\|200px]]	+	==Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations==
		+	<StructureSection load='2yv0' size='340' side='right' caption='[[2yv0]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2yv0]] is a 1 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=2YV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YV0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=2yv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yv0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yv0 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/yv/2yv0_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 ==
		+	A combination of five thermostabilizing mutations, Gly23-->Ala, His62-->Pro, Val74-->Leu, Lys95-->Gly, and Asp134-->His, has been shown to additively enhance the thermostability of Escherichia coli RNase HI [Akasako A, Haruki M, Oobatake M & Kanaya S (1995) Biochemistry34, 8115-8122]. In this study, we determined the crystal structure of the protein with these mutations (5H-RNase HI) to analyze the effects of the mutations on the structure in detail. The structures of the mutation sites were almost identical to those of the mutant proteins to which the mutations were individually introduced, except for G23A, for which the structure of the single mutant protein is not available. Moreover, only slight changes in the backbone conformation of the protein were observed, and the interactions of the side chains were almost conserved. These results indicate that these mutations almost independently affect the protein structure, and are consistent with the fact that the thermostabiling effects of the mutations are cumulative. We also determined the protein stability curve describing the temperature dependence of the free energy of unfolding of 5H-RNase HI to elucidate the thermostabilization mechanism. The maximal stability for 5H-RNase HI was as high as that for the cysteine-free variant of Thermus thermophilus RNase HI. In contrast, the heat capacity of unfolding for 5H-RNase H was similar to that for E. coli RNase HI, which is considerably higher than that for T. thermophilus RNase HI. These results suggest that 5H-RNase HI is stabilized, in part, by the thermostabilization mechanism adopted by T. thermophilus RNase HI.

-	~~{{STRUCTURE_2yv0\| PDB=2yv0 \| SCENE= }}~~	+	Structural and thermodynamic analyses of Escherichia coli RNase HI variant with quintuple thermostabilizing mutations.,Haruki M, Tanaka M, Motegi T, Tadokoro T, Koga Y, Takano K, Kanaya S FEBS J. 2007 Nov;274(22):5815-25. Epub 2007 Oct 18. PMID:17944939<ref>PMID:17944939</ref>

-	~~===Structural and Thermodynamic Analyses~~ of E. ~~coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17944939}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2yv0]] is a 1 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=2YV0 OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017944939<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]

OCA at 15:14, 20 October 2012

OCA — Sat, 20 Oct 2012 15:14:23 GMT

←Older revision		Revision as of 15:14, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2yv0]] is a 1 chain structure ~~of [[Ribonuclease]]~~ 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=2YV0 OCA].	+	[[2yv0]] is a 1 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=2YV0 OCA].

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

OCA: Protected "2yv0" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 17:43:54 GMT

Protected "2yv0" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:43, 26 July 2012

OCA at 17:43, 26 July 2012

OCA — Thu, 26 Jul 2012 17:43:52 GMT

←Older revision		Revision as of 17:43, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2yv0.png\|left\|200px]]		[[Image:2yv0.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2yv0", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2yv0\| PDB=2yv0 \| SCENE= }}		{{STRUCTURE_2yv0\| PDB=2yv0 \| SCENE= }}

	===Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations===		===Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17944939}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17944939 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17944939}}		{{ABSTRACT_PUBMED_17944939}}

	==About this Structure==		==About this Structure==
-	~~2YV0~~ is a 1 chain structure of 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=2YV0 OCA].	+	[[2yv0]] is a 1 chain structure of [[Ribonuclease]] 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=2YV0 OCA].
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17944939~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017944939</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
Line 36:		Line 27:
	[[Category: Quintuple thermostabilizing mutation]]		[[Category: Quintuple thermostabilizing mutation]]
	[[Category: Rnase hi]]		[[Category: Rnase hi]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:57:41 2009''

OCA at 10:57, 17 February 2009

OCA — Tue, 17 Feb 2009 10:57:42 GMT

←Older revision		Revision as of 10:57, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2YV0 is a ~~[[Single protein]]~~ structure of 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=2YV0 OCA].	+	2YV0 is a 1 chain structure of 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=2YV0 OCA].

	==Reference==		==Reference==
-	Structural and thermodynamic analyses of Escherichia coli RNase HI variant with quintuple thermostabilizing mutations., Haruki M, Tanaka M, Motegi T, Tadokoro T, Koga Y, Takano K, Kanaya S, FEBS J. 2007 Nov;274(22):5815-25. Epub 2007 Oct 18. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17944939 17944939]~~	+	<ref group="xtra">PMID:17944939</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
-	[[Category: Single protein]]
	[[Category: Haruki, M.]]		[[Category: Haruki, M.]]
	[[Category: Kanaya, S.]]		[[Category: Kanaya, S.]]
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	[[Category: Rnase hi]]		[[Category: Rnase hi]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28~~ 17:25:~~14 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:57:41 2009''