1slj - Revision history

OCA at 09:08, 22 May 2024

OCA — Wed, 22 May 2024 09:08:53 GMT

←Older revision		Revision as of 09:08, 22 May 2024
Line 19:		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=1slj 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=1slj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K(D) value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme.
		+
		+	Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.,Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP J Mol Biol. 2004 Jul 30;341(1):37-54. PMID:15312761<ref>PMID:15312761</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1slj" 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>

OCA at 08:33, 1 May 2024

OCA — Wed, 01 May 2024 08:33:01 GMT

←Older revision		Revision as of 08:33, 1 May 2024
Line 1:		Line 1:

	==Solution structure of the S1 domain of RNase E from E. coli==		==Solution structure of the S1 domain of RNase E from E. coli==
-	<StructureSection load='1slj' size='340' side='right'caption='[[1slj~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='1slj' size='340' side='right'caption='[[1slj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SLJ 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;'>[[1smx\|1smx]], [[1sn8\|1sn8]]</div></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [https://pdbe.org/1slj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [https://www.ebi.ac.uk/pdbsum/1slj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1slj 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=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [https://pdbe.org/1slj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [https://www.ebi.ac.uk/pdbsum/1slj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1slj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.	+	[https://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
	== 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=1slj 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=1slj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K(D) value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme.
-
-	Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.,Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP J Mol Biol. 2004 Jul 30;341(1):37-54. PMID:15312761<ref>PMID:15312761</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1slj" 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: Cook~~, M A~~]]	+	[[Category: Cook MA]]
-	[[Category: Edge~~, R E~~]]	+	[[Category: Edge RE]]
-	[[Category: Lario, P]]	+	[[Category: Lario P]]
-	[[Category: Mackie~~, G A~~]]	+	[[Category: Mackie GA]]
-	[[Category: McIntosh~~, L P~~]]	+	[[Category: McIntosh LP]]
-	[[Category: Schubert, M]]	+	[[Category: Schubert M]]
-	[[Category: Strynadka~~, N C.J]]~~	+	[[Category: Strynadka NCJ]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ob-fold]]~~	+
-	~~[[Category: Rna-binding~~]]	+

OCA at 06:35, 2 March 2022

OCA — Wed, 02 Mar 2022 06:35:45 GMT

←Older revision		Revision as of 06:35, 2 March 2022
Line 3:		Line 3:
	<StructureSection load='1slj' size='340' side='right'caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1slj' size='340' side='right'caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SLJ 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;'>[[1smx\|1smx]], [[1sn8\|1sn8]]</div></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;'>[[1smx\|1smx]], [[1sn8\|1sn8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [~~http~~://pdbe.org/1slj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1slj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1slj 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=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [https://pdbe.org/1slj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [https://www.ebi.ac.uk/pdbsum/1slj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1slj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.	+	[[https://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	*[[Temp\|Temp]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:29, 24 December 2020

OCA — Thu, 24 Dec 2020 11:29:21 GMT

←Older revision		Revision as of 11:29, 24 December 2020
Line 1:		Line 1:

	==Solution structure of the S1 domain of RNase E from E. coli==		==Solution structure of the S1 domain of RNase E from E. coli==
-	<StructureSection load='1slj' size='340' side='right' caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='1slj' size='340' side='right'caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</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;'>[[1smx\|1smx]], [[1sn8\|1sn8]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://pdbe.org/1slj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1slj 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=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://pdbe.org/1slj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1slj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Cook, M A]]		[[Category: Cook, M A]]
	[[Category: Edge, R E]]		[[Category: Edge, R E]]

OCA at 07:48, 14 March 2018

OCA — Wed, 14 Mar 2018 07:48:13 GMT

←Older revision		Revision as of 07:48, 14 March 2018
Line 1:		Line 1:
		+
	==Solution structure of the S1 domain of RNase E from E. coli==		==Solution structure of the S1 domain of RNase E from E. coli==
	<StructureSection load='1slj' size='340' side='right' caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1slj' size='340' side='right' caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://pdbe.org/1slj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj 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=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://pdbe.org/1slj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1slj 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/sl/1slj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sl/1slj_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 16:56, 8 February 2016

OCA — Mon, 08 Feb 2016 16:56:04 GMT

←Older revision		Revision as of 16:56, 8 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=1slj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:36, 10 September 2015

OCA — Thu, 10 Sep 2015 13:36:01 GMT

←Older revision		Revision as of 13:36, 10 September 2015
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	<StructureSection load='1slj' size='340' side='right' caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1slj' size='340' side='right' caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj 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=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://pdbe.org/1slj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj 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 1slj" 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: Cook, M A]]		[[Category: Cook, M A]]
	[[Category: Edge, R E]]		[[Category: Edge, R E]]

OCA at 00:49, 25 December 2014

OCA — Thu, 25 Dec 2014 00:49:19 GMT

←Older revision		Revision as of 00:49, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj 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=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
	== 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\|Ribonuclease]]
		+	*[[Temp\|Temp]]
		+	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Cook, M A.]]	+	[[Category: Cook, M A]]
-	[[Category: Edge, R E.]]	+	[[Category: Edge, R E]]
-	[[Category: Lario, P.]]	+	[[Category: Lario, P]]
-	[[Category: Mackie, G A.]]	+	[[Category: Mackie, G A]]
-	[[Category: McIntosh, L P.]]	+	[[Category: McIntosh, L P]]
-	[[Category: Schubert, M.]]	+	[[Category: Schubert, M]]
-	[[Category: Strynadka, N C.J.]]	+	[[Category: Strynadka, N C.J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Ob-fold]]		[[Category: Ob-fold]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]

OCA at 22:26, 28 September 2014

OCA — Sun, 28 Sep 2014 22:26:19 GMT

←Older revision		Revision as of 22:26, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1slj.~~png~~\|~~left~~\|200px]]	+	==Solution structure of the S1 domain of RNase E from E. coli==
		+	<StructureSection load='1slj' size='340' side='right' caption='[[1slj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SLJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1smx\|1smx]], [[1sn8\|1sn8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1slj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1slj RCSB], [http://www.ebi.ac.uk/pdbsum/1slj 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/sl/1slj_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 ==
		+	S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K(D) value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme.

-	~~{{STRUCTURE_1slj\| PDB=1slj \| SCENE= }}~~	+	Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.,Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP J Mol Biol. 2004 Jul 30;341(1):37-54. PMID:15312761<ref>PMID:15312761</ref>

-	~~===Solution structure~~ of the ~~S1 domain~~ of ~~RNase E from E~~. ~~coli===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15312761}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1slj]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015312761<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Cook, M A.]]		[[Category: Cook, M A.]]

OCA at 10:49, 20 October 2012

OCA — Sat, 20 Oct 2012 10:49:36 GMT

←Older revision		Revision as of 10:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1slj]] is a 1 chain structure ~~of [[Ribonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA].	+	[[1slj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLJ OCA].

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