2mf0: Difference between revisions

Latest revision as of 07:00, 1 May 2024

Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex

Structural highlights

2mf0 is a 7 chain structure with sequence from Pseudomonas fluorescens and Pseudomonas protegens Pf-5. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

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:https://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:https://dx.doi.org/10.1038/nature13271

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OCA

[1] 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

[2] 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

[3] 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

[4] 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

[5] 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:https://dx.doi.org/10.1093/nar/gku141

[6] 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:https://dx.doi.org/10.1038/nature13271

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 2mf0 is ON HOLD
+==Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex==
+<StructureSection load='2mf0' size='340' side='right'caption='[[2mf0]]' scene=''>
-Authors: Duss, O., Michel, E., Yulikov, M., Schubert, M., Jeschke, G., Allain, F.H.-T.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2mf0]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens] and [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MF0 FirstGlance]. <br>
-Description: Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex
+</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=2mf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mf0 OCA], [https://pdbe.org/2mf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mf0 RCSB], [https://www.ebi.ac.uk/pdbsum/2mf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mf0 ProSAT]</span></td></tr>
+</table>
+== 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>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pseudomonas fluorescens]]
+[[Category: Pseudomonas protegens Pf-5]]
+[[Category: Allain FH-T]]
+[[Category: Duss O]]
+[[Category: Jeschke G]]
+[[Category: Michel E]]
+[[Category: Schubert M]]
+[[Category: Yulikov M]]

2mf0: Difference between revisions

Latest revision as of 07:00, 1 May 2024

Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex

Structural highlights

Function

References

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