2mfh - Revision history

OCA at 07:00, 1 May 2024

OCA — Wed, 01 May 2024 07:00:12 GMT

←Older revision		Revision as of 07:00, 1 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MFH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MFH FirstGlance]. <br>
-	</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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [https://pdbe.org/2mfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [https://www.ebi.ac.uk/pdbsum/2mfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mfh ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [https://pdbe.org/2mfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [https://www.ebi.ac.uk/pdbsum/2mfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mfh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CSRA1_PSEPH CSRA1_PSEPH] A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability (PubMed:17704818, PubMed:23635605). Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer and each dimer could bind the same mRNA twice (PubMed:17704818). Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome binding (PubMed:17704818, PubMed:24561806, PubMed:23635605). Overexpression represses target protein expression; mutating nucleotides in the 5' UTR abolishes repression in vivo (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequences in loops to which the CsrA proteins bind (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA sequences in RsmZ in a defined order (PubMed:24828038, PubMed:24561806). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four CsrA1 dimers maximally protect RsmZ from RNase activity (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no detectable phenotype, but a double rsmY-rsmZ deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and protects cucumber plants from fungal infection less well than wild-type; the triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).<ref>PMID:15601712</ref> <ref>PMID:16286659</ref> <ref>PMID:17704818</ref> <ref>PMID:23635605</ref> <ref>PMID:24561806</ref> <ref>PMID:24828038</ref>		[https://www.uniprot.org/uniprot/CSRA1_PSEPH CSRA1_PSEPH] A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability (PubMed:17704818, PubMed:23635605). Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer and each dimer could bind the same mRNA twice (PubMed:17704818). Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome binding (PubMed:17704818, PubMed:24561806, PubMed:23635605). Overexpression represses target protein expression; mutating nucleotides in the 5' UTR abolishes repression in vivo (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequences in loops to which the CsrA proteins bind (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA sequences in RsmZ in a defined order (PubMed:24828038, PubMed:24561806). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four CsrA1 dimers maximally protect RsmZ from RNase activity (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no detectable phenotype, but a double rsmY-rsmZ deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and protects cucumber plants from fungal infection less well than wild-type; the triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).<ref>PMID:15601712</ref> <ref>PMID:16286659</ref> <ref>PMID:17704818</ref> <ref>PMID:23635605</ref> <ref>PMID:24561806</ref> <ref>PMID:24828038</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude ( approximately 10 nM to approximately 3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.
-
-	Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.,Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH Nucleic Acids Res. 2014 Feb 21. PMID:24561806<ref>PMID:24561806</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2mfh" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:34, 2 March 2023

OCA — Thu, 02 Mar 2023 06:34:12 GMT

←Older revision		Revision as of 06:34, 2 March 2023
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	==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex==		==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex==
-	<StructureSection load='2mfh' size='340' side='right'caption='[[2mfh~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2mfh' size='340' side='right'caption='[[2mfh]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus~~ fluorescens ~~liquefaciens" flugge 1886~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MFH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MFH 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;'>[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</div></td></tr>	+	</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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [https://pdbe.org/2mfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [https://www.ebi.ac.uk/pdbsum/2mfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mfh ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [https://pdbe.org/2mfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [https://www.ebi.ac.uk/pdbsum/2mfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mfh ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~Q5MXB2_PSEFL Q5MXB2_PSEFL~~]~~] Could accelerate~~ the ~~degradation~~ of ~~some~~ genes ~~transcripts potentially through selective RNA~~ binding (~~By similarity~~).~~[HAMAP~~-~~Rule~~:~~MF_00167][SAAS~~:~~SAAS003751_004_007709]~~	+	[https://www.uniprot.org/uniprot/CSRA1_PSEPH CSRA1_PSEPH] A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability (PubMed:17704818, PubMed:23635605). Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer and each dimer could bind the same mRNA twice (PubMed:17704818). Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome binding (PubMed:17704818, PubMed:24561806, PubMed:23635605). Overexpression represses target protein expression; mutating nucleotides in the 5' UTR abolishes repression in vivo (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequences in loops to which the CsrA proteins bind (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA sequences in RsmZ in a defined order (PubMed:24828038, PubMed:24561806). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four CsrA1 dimers maximally protect RsmZ from RNase activity (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no detectable phenotype, but a double rsmY-rsmZ deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and protects cucumber plants from fungal infection less well than wild-type; the triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).<ref>PMID:15601712</ref> <ref>PMID:16286659</ref> <ref>PMID:17704818</ref> <ref>PMID:23635605</ref> <ref>PMID:24561806</ref> <ref>PMID:24828038</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Allain, F H.T~~]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: ~~Duss, O~~]]	+	[[Category: Allain FH-T]]
-	[[Category: Konte, N ~~Diarra Dit~~]]	+	[[Category: Diarra Dit Konte N]]
-	[[Category: ~~Michel, E~~]]	+	[[Category: Duss O]]
-	[[Category: ~~Schubert, M~~]]	+	[[Category: Michel E]]
-	[[Category: ~~Bacterial protein]]~~	+	[[Category: Schubert M]]
-	~~[[Category: Csra]]~~	+
-	~~[[Category: Csrb]]~~	+
-	~~[[Category: Messenger rna]]~~	+
-	~~[[Category: Modulation of binding affinity]]~~	+
-	~~[[Category: Molecular mimicry]]~~	+
-	~~[[Category: Non-coding rna]]~~	+
-	~~[[Category: Protein sequestration]]~~	+
-	~~[[Category: Pseudomonas aeruginosa]]~~	+
-	~~[[Category: Rna-binding protein]]~~	+
-	~~[[Category: Rsma]]~~	+
-	~~[[Category: Rsme]]~~	+
-	~~[[Category: Rsmz]]~~	+
-	~~[[Category: Srna]]~~	+
-	~~[[Category: Translation activation]]~~	+
-	~~[[Category: Translation repressor protein]]~~	+
-	~~[[Category: Translation-rna complex~~]]	+

OCA at 10:09, 26 May 2021

OCA — Wed, 26 May 2021 10:09:17 GMT

←Older revision		Revision as of 10:09, 26 May 2021
Line 1:		Line 1:

	==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex==		==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex==
-	<StructureSection load='2mfh' size='340' side='right' caption='[[2mfh]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2mfh' size='340' side='right'caption='[[2mfh]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2MFH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MFH FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</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;'>[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [~~http~~://pdbe.org/2mfh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2mfh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2mfh 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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [https://pdbe.org/2mfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [https://www.ebi.ac.uk/pdbsum/2mfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mfh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/Q5MXB2_PSEFL Q5MXB2_PSEFL]] Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity).[HAMAP-Rule:MF_00167][SAAS:SAAS003751_004_007709]	+	[[https://www.uniprot.org/uniprot/Q5MXB2_PSEFL Q5MXB2_PSEFL]] Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity).[HAMAP-Rule:MF_00167][SAAS:SAAS003751_004_007709]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]		[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Allain, F H.T]]		[[Category: Allain, F H.T]]
	[[Category: Duss, O]]		[[Category: Duss, O]]

OCA at 22:30, 9 August 2018

OCA — Thu, 09 Aug 2018 22:30:40 GMT

←Older revision		Revision as of 22:30, 9 August 2018
Line 1:		Line 1:
		+
	==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex==		==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex==
	<StructureSection load='2mfh' size='340' side='right' caption='[[2mfh]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2mfh' size='340' side='right' caption='[[2mfh]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [http://pdbe.org/2mfh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [http://www.ebi.ac.uk/pdbsum/2mfh 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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [http://pdbe.org/2mfh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [http://www.ebi.ac.uk/pdbsum/2mfh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2mfh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:58, 11 September 2015

OCA — Fri, 11 Sep 2015 08:58:32 GMT

←Older revision		Revision as of 08:58, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [http://www.ebi.ac.uk/pdbsum/2mfh 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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [http://pdbe.org/2mfh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [http://www.ebi.ac.uk/pdbsum/2mfh PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	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 2mfh" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:10, 25 December 2014

OCA — Thu, 25 Dec 2014 14:10:42 GMT

←Older revision		Revision as of 14:10, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='2mfh' size='340' side='right' caption='[[2mfh]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2mfh' size='340' side='right' caption='[[2mfh]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. <br>	+	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MFH FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [http://www.ebi.ac.uk/pdbsum/2mfh PDBsum]</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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [http://www.ebi.ac.uk/pdbsum/2mfh PDBsum]</span></td></tr>	+	</table>
-	<table>	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q5MXB2_PSEFL Q5MXB2_PSEFL]] Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity).[HAMAP-Rule:MF_00167][SAAS:SAAS003751_004_007709]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 15:
	Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.,Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH Nucleic Acids Res. 2014 Feb 21. PMID:24561806<ref>PMID:24561806</ref>		Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.,Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH Nucleic Acids Res. 2014 Feb 21. PMID:24561806<ref>PMID:24561806</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]		[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
-	[[Category: Allain, F H.T.]]	+	[[Category: Allain, F H.T]]
-	[[Category: Duss, O.]]	+	[[Category: Duss, O]]
-	[[Category: Konte, N Diarra Dit.]]	+	[[Category: Konte, N Diarra Dit]]
-	[[Category: Michel, E.]]	+	[[Category: Michel, E]]
-	[[Category: Schubert, M.]]	+	[[Category: Schubert, M]]
	[[Category: Bacterial protein]]		[[Category: Bacterial protein]]
	[[Category: Csra]]		[[Category: Csra]]

OCA at 06:43, 14 May 2014

OCA — Wed, 14 May 2014 06:43:41 GMT

←Older revision		Revision as of 06:43, 14 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2mfh\| PDB=2mfh \| SCENE= }}~~	+	==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex==
-	===Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex===	+	<StructureSection load='2mfh' size='340' side='right' caption='[[2mfh]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_24561806}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2mfh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mfc\|2mfc]], [[2mfe\|2mfe]], [[2mff\|2mff]], [[2mfg\|2mfg]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2mfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mfh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mfh RCSB], [http://www.ebi.ac.uk/pdbsum/2mfh PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude ( approximately 10 nM to approximately 3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.

-	~~==Function==~~	+	Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.,Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH Nucleic Acids Res. 2014 Feb 21. PMID:24561806<ref>PMID:24561806</ref>
-	~~[[http://www.uniprot.org/uniprot/Q5MXB2_PSEFL Q5MXB2_PSEFL]] Could accelerate~~ the ~~degradation~~ of ~~some genes transcripts potentially through selective~~ RNA ~~binding (By similarity)~~.~~[HAMAP-Rule~~:~~MF_00167][SAAS~~:~~SAAS003751_004_007709]~~	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2mfh]] is~~ a ~~4 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2MFH OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024561806</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Allain, F H.T.]]		[[Category: Allain, F H.T.]]
	[[Category: Duss, O.]]		[[Category: Duss, O.]]

OCA at 06:11, 26 March 2014

OCA — Wed, 26 Mar 2014 06:11:39 GMT

←Older revision		Revision as of 06:11, 26 March 2014
Line 1:		Line 1:
	{{STRUCTURE_2mfh\| PDB=2mfh \| SCENE= }}		{{STRUCTURE_2mfh\| PDB=2mfh \| SCENE= }}
	===Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex===		===Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex===
		+	{{ABSTRACT_PUBMED_24561806}}

	==Function==		==Function==
Line 7:		Line 8:
	==About this Structure==		==About this Structure==
	[[2mfh]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA].		[[2mfh]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024561806</ref><references group="xtra"/><references/>
	[[Category: Allain, F H.T.]]		[[Category: Allain, F H.T.]]
	[[Category: Duss, O.]]		[[Category: Duss, O.]]

OCA at 18:16, 3 March 2014

OCA — Mon, 03 Mar 2014 18:16:54 GMT

←Older revision		Revision as of 18:16, 3 March 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_2mfh\| PDB=2mfh \| SCENE= }}
		+	===Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex===

-	~~The entry 2mfh is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/Q5MXB2_PSEFL Q5MXB2_PSEFL]] Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity).[HAMAP-Rule:MF_00167][SAAS:SAAS003751_004_007709]

-	~~Authors~~: Duss, O.~~, Diarra Dit~~ Konte, N., Michel, E., Schubert, M.~~, Allain, F.H.-T.~~	+	==About this Structure==
-		+	[[2mfh]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFH OCA].
-	~~Description~~: ~~Csr/Rsm~~ protein~~-RNA recognition -A molecular~~ affinity ~~ruler~~: ~~RsmZ(36~~-~~44)/RsmE(dimer) 2~~:1 complex	+	[[Category: Allain, F H.T.]]
		+	[[Category: Duss, O.]]
		+	[[Category: Konte, N Diarra Dit.]]
		+	[[Category: Michel, E.]]
		+	[[Category: Schubert, M.]]
		+	[[Category: Bacterial protein]]
		+	[[Category: Csra]]
		+	[[Category: Csrb]]
		+	[[Category: Messenger rna]]
		+	[[Category: Modulation of binding affinity]]
		+	[[Category: Molecular mimicry]]
		+	[[Category: Non-coding rna]]
		+	[[Category: Protein sequestration]]
		+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Rna-binding protein]]
		+	[[Category: Rsma]]
		+	[[Category: Rsme]]
		+	[[Category: Rsmz]]
		+	[[Category: Srna]]
		+	[[Category: Translation activation]]
		+	[[Category: Translation repressor protein]]
		+	[[Category: Translation-rna complex]]

OCA at 06:34, 22 January 2014

OCA — Wed, 22 Jan 2014 06:34:23 GMT

←Older revision		Revision as of 06:34, 22 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 2mfh is ON HOLD	+	The entry 2mfh is ON HOLD until Paper Publication

	Authors: Duss, O., Diarra Dit Konte, N., Michel, E., Schubert, M., Allain, F.H.-T.		Authors: Duss, O., Diarra Dit Konte, N., Michel, E., Schubert, M., Allain, F.H.-T.

	Description: Csr/Rsm protein-RNA recognition -A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex		Description: Csr/Rsm protein-RNA recognition -A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex