7A05

NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1

Summary for 7A05

• Entry DOI: 10.2210/pdb7a05/pdb
• NMR Information: BMRB: 34549
• Descriptor: 30S ribosomal protein S1 (1 entity in total)
• Functional Keywords: ribosomal protein s1 domain 3 and domain 4 vibrio vulnificus ob-fold mrna binding rs1-d34, ribosomal protein
• Biological source: Vibrio vulnificus
• Total number of polymer chains: 1
• Total formula weight: 19393.11

Authors

Qureshi, N.S.,Matzel, T.,Cetiner, E.C.,Schnieders, S.,Jonker, H.R.A.,Schwalbe, H.,Fuertig, B. (deposition date: 2020-08-06, release date: 2021-06-23, Last modification date: 2024-01-17)

Primary citation

Qureshi, N.S.,Matzel, T.,Cetiner, E.C.,Schnieders, R.,Jonker, H.R.A.,Schwalbe, H.,Furtig, B.
NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs.
Nucleic Acids Res., 49:7753-7764, 2021

PubMed Abstract: The ribosomal S1 protein (rS1) is indispensable for translation initiation in Gram-negative bacteria. rS1 is a multidomain protein that acts as an RNA chaperone and ensures that mRNAs can bind the ribosome in a single-stranded conformation, which could be related to fast recognition. Although many ribosome structures were solved in recent years, a high-resolution structure of a two-domain mRNA-binding competent rS1 construct is not yet available. Here, we present the NMR solution structure of the minimal mRNA-binding fragment of Vibrio Vulnificus rS1 containing the domains D3 and D4. Both domains are homologues and adapt an oligonucleotide-binding fold (OB fold) motif. NMR titration experiments reveal that recognition of miscellaneous mRNAs occurs via a continuous interaction surface to one side of these structurally linked domains. Using a novel paramagnetic relaxation enhancement (PRE) approach and exploring different spin-labeling positions within RNA, we were able to track the location and determine the orientation of the RNA in the rS1-D34 bound form. Our investigations show that paramagnetically labeled RNAs, spiked into unmodified RNA, can be used as a molecular ruler to provide structural information on protein-RNA complexes. The dynamic interaction occurs on a defined binding groove spanning both domains with identical β2-β3-β5 interfaces. Evidently, the 3'-ends of the cis-acting RNAs are positioned in the direction of the N-terminus of the rS1 protein, thus towards the 30S binding site and adopt a conformation required for translation initiation.

PubMed: 34223902
DOI: 10.1093/nar/gkab562

Experimental method

SOLUTION NMR