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| | ==Structural basis of RsmA/CsrA RNA recognition: Structure of RsmE bound to the Shine-Dalgarno sequence of hcnA mRNA== | | ==Structural basis of RsmA/CsrA RNA recognition: Structure of RsmE bound to the Shine-Dalgarno sequence of hcnA mRNA== |
| - | <StructureSection load='2jpp' size='340' side='right' caption='[[2jpp]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='2jpp' size='340' side='right'caption='[[2jpp]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2jpp]] 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=2JPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JPP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2jpp]] 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=2JPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JPP FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rsmE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jpp OCA], [http://pdbe.org/2jpp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jpp RCSB], [http://www.ebi.ac.uk/pdbsum/2jpp PDBsum]</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=2jpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jpp OCA], [https://pdbe.org/2jpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jpp RCSB], [https://www.ebi.ac.uk/pdbsum/2jpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jpp 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/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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jp/2jpp_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jp/2jpp_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> |
| | </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=2jpp ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus fluorescens liquefaciens flugge 1886]] | + | [[Category: Large Structures]] |
| - | [[Category: Allain, F H.T]] | + | [[Category: Pseudomonas fluorescens]] |
| - | [[Category: Duss, O]] | + | [[Category: Allain FH-T]] |
| - | [[Category: Haas, D]] | + | [[Category: Duss O]] |
| - | [[Category: Jelesarov, I]] | + | [[Category: Haas D]] |
| - | [[Category: Lapouge, K]] | + | [[Category: Jelesarov I]] |
| - | [[Category: Oberstrass, F C]] | + | [[Category: Lapouge K]] |
| - | [[Category: Schubert, M]] | + | [[Category: Oberstrass FC]] |
| - | [[Category: Csra]]
| + | [[Category: Schubert M]] |
| - | [[Category: Protein/rna]]
| + | |
| - | [[Category: Rna recognition]]
| + | |
| - | [[Category: Rsma]]
| + | |
| - | [[Category: Shine-dalgarno]]
| + | |
| - | [[Category: Translation-rna complex]]
| + | |
| Structural highlights
Function
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).[1] [2] [3] [4] [5] [6]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Proteins of the RsmA/CsrA family are global translational regulators in many bacterial species. We have determined the solution structure of a complex formed between the RsmE protein, a member of this family from Pseudomonas fluorescens, and a target RNA encompassing the ribosome-binding site of the hcnA gene. The RsmE homodimer with its two RNA-binding sites makes optimal contact with an 5'-A/UCANGGANGU/A-3' sequence in the mRNA. When tightly gripped by RsmE, the ANGGAN core folds into a loop, favoring the formation of a 3-base-pair stem by flanking nucleotides. We validated these findings by in vivo and in vitro mutational analyses. The structure of the complex explains well how, by sequestering the Shine-Dalgarno sequence, the RsmA/CsrA proteins repress translation.
Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA.,Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH Nat Struct Mol Biol. 2007 Sep;14(9):807-13. Epub 2007 Aug 19. PMID:17704818[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Reimmann C, Valverde C, Kay E, Haas D. Posttranscriptional repression of GacS/GacA-controlled genes by the RNA-binding protein RsmE acting together with RsmA in the biocontrol strain Pseudomonas fluorescens CHA0. J Bacteriol. 2005 Jan;187(1):276-85. PMID:15601712 doi:10.1128/JB.187.1.276-285.2005
- ↑ Kay E, Dubuis C, Haas D. Three small RNAs jointly ensure secondary metabolism and biocontrol in Pseudomonas fluorescens CHA0. Proc Natl Acad Sci U S A. 2005 Nov 22;102(47):17136-41. PMID:16286659 doi:10.1073/pnas.0505673102
- ↑ Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH. Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nat Struct Mol Biol. 2007 Sep;14(9):807-13. Epub 2007 Aug 19. PMID:17704818 doi:10.1038/nsmb1285
- ↑ Lapouge K, Perozzo R, Iwaszkiewicz J, Bertelli C, Zoete V, Michielin O, Scapozza L, Haas D. RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family. RNA Biol. 2013 Jun;10(6):1031-41. PMID:23635605 doi:10.4161/rna.24771
- ↑ Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH. Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition. Nucleic Acids Res. 2014 Feb 21. PMID:24561806 doi:http://dx.doi.org/10.1093/nar/gku141
- ↑ Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FH. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature. 2014 May 29;509(7502):588-92. doi: 10.1038/nature13271. Epub 2014 May 14. PMID:24828038 doi:http://dx.doi.org/10.1038/nature13271
- ↑ Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH. Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nat Struct Mol Biol. 2007 Sep;14(9):807-13. Epub 2007 Aug 19. PMID:17704818 doi:10.1038/nsmb1285
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