1jxb - Revision history

OCA at 07:42, 7 February 2024

2024-02-07T07:42:39Z

←Older revision		Revision as of 07:42, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1jxb' size='340' side='right'caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1jxb' size='340' side='right'caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JXB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JXB FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[1f21\|1f21]]~~, [[~~1jl1~~\|~~1jl1~~]]~~</div></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]] 1.6Å</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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [https://pdbe.org/1jxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [https://www.ebi.ac.uk/pdbsum/1jxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jxb 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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [https://pdbe.org/1jxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [https://www.ebi.ac.uk/pdbsum/1jxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jxb 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]]
Line 20:		Line 19:
	</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=1jxb 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=1jxb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A point mutation (I53A) in the core of Escherichia coli RNase H* is known to destabilize both the native conformation (DeltaG(UN)) and the kinetic intermediate (DeltaG(UI)) by 2 kcal/mole. Here, we have used native-state hydrogen deuterium exchange to ask how this destabilization is propagated throughout the molecule. Stability parameters were obtained for individual residues in I53A and compared with those from the wild-type protein. A destabilization of 2 kcal/mole was observed in residues in the core but was not detected in the periphery of the molecule. These results are consistent with the localized destabilization of the core observed in the early intermediate of the kinetic folding pathway, supporting the resemblance of this kinetic intermediate to the partially unfolded form detected in the native state at equilibrium. A thermodynamic cycle also shows no interaction between Ile 53 and a residue in the periphery. There is, however, an increase in the number of denaturant-independent exchange events in the periphery of I53A, showing that effects of the point mutation are communicated to regions outside the core, although perhaps not through changes in stability. In sum, this work shows that localized regions within a protein can be destabilized independently. Furthermore, it implies a correspondence between the kinetic intermediate and the equilibrium PUF, as the magnitude and localization of the destabilization are the same in both.
-
-	Propagation of a single destabilizing mutation throughout the Escherichia coli ribonuclease HI native state.,Spudich G, Lorenz S, Marqusee S Protein Sci. 2002 Mar;11(3):522-8. PMID:11847275<ref>PMID:11847275</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1jxb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonuclease H]]~~	+	[[Category: Lorenz S]]
-	[[Category: Lorenz, S]]	+	[[Category: Marqusee S]]
-	[[Category: Marqusee, S]]	+	[[Category: Spudich G]]
-	[[Category: Spudich, G]]	+
-	~~[[Category: 4-helix bundle]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mixed alpha/beta~~]]	+

OCA at 06:46, 11 August 2021

2021-08-11T06:46:38Z

←Older revision		Revision as of 06:46, 11 August 2021
Line 3:		Line 3:
	<StructureSection load='1jxb' size='340' side='right'caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1jxb' size='340' side='right'caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JXB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JXB FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f21\|1f21]], [[1jl1\|1jl1]]</div></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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [~~http~~://pdbe.org/1jxb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jxb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jxb 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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [https://pdbe.org/1jxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [https://www.ebi.ac.uk/pdbsum/1jxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jxb 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]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	*[[Temp\|Temp]]	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:36, 6 November 2019

2019-11-06T09:36:58Z

←Older revision		Revision as of 09:36, 6 November 2019
Line 1:		Line 1:

	==I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI==		==I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI==
-	<StructureSection load='1jxb' size='340' side='right' caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1jxb' size='340' side='right'caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JXB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JXB FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==
Line 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Lorenz, S]]		[[Category: Lorenz, S]]

OCA at 09:11, 17 January 2018

2018-01-17T09:11:46Z

←Older revision		Revision as of 09:11, 17 January 2018
Line 1:		Line 1:
		+
	==I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI==		==I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI==
	<StructureSection load='1jxb' size='340' side='right' caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1jxb' size='340' side='right' caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [http://pdbe.org/1jxb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [http://www.ebi.ac.uk/pdbsum/1jxb 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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [http://pdbe.org/1jxb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [http://www.ebi.ac.uk/pdbsum/1jxb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jxb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jx/1jxb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jx/1jxb_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>
Line 30:		Line 31:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==

OCA at 06:42, 9 February 2016

2016-02-09T06:42:32Z

←Older revision		Revision as of 06:42, 9 February 2016
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=1jxb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:36, 10 September 2015

2015-09-10T19:36:59Z

←Older revision		Revision as of 19:36, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1jxb' size='340' side='right' caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1jxb' size='340' side='right' caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JXB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JXB FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [http://www.ebi.ac.uk/pdbsum/1jxb 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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [http://pdbe.org/1jxb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [http://www.ebi.ac.uk/pdbsum/1jxb PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1jxb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Lorenz, S]]		[[Category: Lorenz, S]]

OCA at 12:08, 5 March 2015

2015-03-05T12:08:47Z

←Older revision		Revision as of 12:08, 5 March 2015
Line 31:		Line 31:
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
-	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:07, 25 December 2014

2014-12-25T05:07:14Z

←Older revision		Revision as of 05:07, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JXB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JXB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [http://www.ebi.ac.uk/pdbsum/1jxb 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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [http://www.ebi.ac.uk/pdbsum/1jxb 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: Lorenz, S.]]	+	[[Category: Lorenz, S]]
-	[[Category: Marqusee, S.]]	+	[[Category: Marqusee, S]]
-	[[Category: Spudich, G.]]	+	[[Category: Spudich, G]]
	[[Category: 4-helix bundle]]		[[Category: 4-helix bundle]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Mixed alpha/beta]]		[[Category: Mixed alpha/beta]]

OCA at 12:10, 28 September 2014

2014-09-28T12:10:51Z

←Older revision		Revision as of 12:10, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1jxb.~~png~~\|~~left~~\|200px]]	+	==I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI==
		+	<StructureSection load='1jxb' size='340' side='right' caption='[[1jxb]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JXB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f21\|1f21]], [[1jl1\|1jl1]]</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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [http://www.ebi.ac.uk/pdbsum/1jxb 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/jx/1jxb_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 point mutation (I53A) in the core of Escherichia coli RNase H* is known to destabilize both the native conformation (DeltaG(UN)) and the kinetic intermediate (DeltaG(UI)) by 2 kcal/mole. Here, we have used native-state hydrogen deuterium exchange to ask how this destabilization is propagated throughout the molecule. Stability parameters were obtained for individual residues in I53A and compared with those from the wild-type protein. A destabilization of 2 kcal/mole was observed in residues in the core but was not detected in the periphery of the molecule. These results are consistent with the localized destabilization of the core observed in the early intermediate of the kinetic folding pathway, supporting the resemblance of this kinetic intermediate to the partially unfolded form detected in the native state at equilibrium. A thermodynamic cycle also shows no interaction between Ile 53 and a residue in the periphery. There is, however, an increase in the number of denaturant-independent exchange events in the periphery of I53A, showing that effects of the point mutation are communicated to regions outside the core, although perhaps not through changes in stability. In sum, this work shows that localized regions within a protein can be destabilized independently. Furthermore, it implies a correspondence between the kinetic intermediate and the equilibrium PUF, as the magnitude and localization of the destabilization are the same in both.

-	~~{{STRUCTURE_1jxb\| PDB=1jxb \| SCENE= }}~~	+	Propagation of a single destabilizing mutation throughout the Escherichia coli ribonuclease HI native state.,Spudich G, Lorenz S, Marqusee S Protein Sci. 2002 Mar;11(3):522-8. PMID:11847275<ref>PMID:11847275</ref>

-	~~===I53A~~, a ~~point mutant~~ of the ~~cysteine-free variant~~ of E. ~~coli Rnase HI===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11847275}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1jxb]] 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=1JXB OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011847275<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]

OCA at 13:00, 20 October 2012

2012-10-20T13:00:08Z

←Older revision		Revision as of 13:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1jxb]] 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=1JXB OCA].	+	[[1jxb]] 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=1JXB OCA].

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