2MFH

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

Summary for 2MFH

• Entry DOI: 10.2210/pdb2mfh/pdb
• Related: 2MFC 2MFE 2MFF 2MFG
• NMR Information: BMRB: 19549
• Descriptor: Carbon storage regulator homolog, RsmZ(36-44) RNA (2 entities in total)
• Functional Keywords: csra, rsma, rsme, rsmz, csrb, translation repressor protein, translation activation, protein sequestration, bacterial protein, non-coding rna, srna, pseudomonas aeruginosa, rna-binding proteins, messenger rna, modulation of binding affinity, molecular mimicry, translation-rna complex, translation/rna
• Biological source: Pseudomonas fluorescens
• Total number of polymer chains: 4
• Total formula weight: 21407.44

Authors

Duss, O.,Diarra Dit Konte, N.,Michel, E.,Schubert, M.,Allain, F.H.-T. (deposition date: 2013-10-11, release date: 2014-02-26, Last modification date: 2024-05-01)

Primary citation

Duss, O.,Michel, E.,Diarra Dit Konte, N.,Schubert, M.,Allain, F.H.
Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.
Nucleic Acids Res., 42:5332-5346, 2014

PubMed Abstract: 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 (∼10 nM to ∼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.

PubMed: 24561806
DOI: 10.1093/nar/gku141

Experimental method

SOLUTION NMR