9QH3
Pseudomonas aeruginosa polynucleotide phosphorylase in complex with recognition site of RNase E
Summary for 9QH3
| Entry DOI | 10.2210/pdb9qh3/pdb |
| EMDB information | 53153 |
| Descriptor | Polyribonucleotide nucleotidyltransferase, Ribonuclease E, ADENOSINE-5'-MONOPHOSPHATE, ... (4 entities in total) |
| Functional Keywords | polynucleotide phosphorylase, ribonuclease e, rna degradosome, rna binding protein |
| Biological source | Pseudomonas aeruginosa PAO1 More |
| Total number of polymer chains | 4 |
| Total formula weight | 183136.53 |
| Authors | Paris, G.,Luisi, B.F. (deposition date: 2025-03-14, release date: 2025-05-14, Last modification date: 2025-11-26) |
| Primary citation | Paris, G.,Katsuya-Gaviria, K.,Clarke, H.,Johncock, M.,Dendooven, T.,Lulla, A.,Luisi, B.F. A multi-dentate, cooperative interaction between endo- and exo-ribonucleases within the bacterial RNA degradosome. Nucleic Acids Res., 53:-, 2025 Cited by PubMed Abstract: In Escherichia coli and numerous other bacteria, two of the principal enzymes mediating messenger RNA decay and RNA processing-RNase E, an endoribonuclease, and polynucleotide phosphorylase (PNPase), an exoribonuclease-assemble into a multi-enzyme complex known as the RNA degradosome. While RNase E forms a homotetramer and PNPase a homotrimer, it remains unclear how these two enzymes interact within the RNA degradosome to potentially satisfy all mutual recognition sites. In this study, we used cryo-EM, biochemistry, and biophysical studies to discover and characterize a new binding mode for PNPase encompassing two or more motifs that are necessary and sufficient for strong interaction with RNase E. While a similar interaction is seen in Salmonella enterica, a different recognition mode arose for Pseudomonas aeruginosa, illustrating the evolutionary drive to maintain physical association of the two ribonucleases. The data presented here suggest a model for the quaternary organization of the RNA degradosome of E. coli, where one PNPase trimer interacts with one RNase E protomer. Conformational transitions are predicted to facilitate substrate capture and transfer to catalytic centres. The model suggests how the endo- and exo-ribonucleases might cooperate in cellular RNA turnover and recruitment of regulatory RNA by the degradosome assembly. PubMed: 41036625DOI: 10.1093/nar/gkaf960 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.4 Å) |
Structure validation
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