Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Can also process other RNA species, such as RNAI, a molecule that controls the replication of ColE1 plasmid, and the cell division inhibitor DicF-RNA. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process. Required to initiate rRNA degradation during both starvation and quality control; acts after RNase PH (rph) exonucleolytically digests the 3'-end of the 16S rRNA (PubMed:27298395). Degradation of 16S rRNA leads to 23S rRNA degradation (PubMed:27298395). Processes the 3 tRNA(Pro) precursors immediately after the 3'-CCA to generate the mature ends (PubMed:27288443). Prefers 5'-monophosphorylated substrates over 5'-triphosphorylated substrates (PubMed:10762247). 5'-monophosphate-assisted cleavage requires at least 2 and preferably 3 or more unpaired 5'-terminal nucleotides. The optimal spacing between the 5' end and the scissile phosphate appears to be 8 nucleotides. Any sequence of unpaired nucleotides at the 5'-end is tolerated (PubMed:26694614). Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions. Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between subunits and are essential for homotetramerization and catalytic activity, but not for RNA binding. In the absence of zinc, the protein dissociates into inactive dimers. Binds 1 Mg(2+) ion per subunit. The presence of a 5'-monophosphate on substrate RNA accelerates its cleavage by catalytically activating the enzyme (PubMed:15197283). Binding to the membrane stabilizes protein structure and increases affinity for the substrate. kcat is 0.83 min(-1) for 5'-PO(4) substrate and 0.088 min(-1) for 5-OH substrate. Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Within the RNA degradosome, RNase E assembles into a homotetramer formed by a dimer of dimers. Tetramerization is essential for catalytic activity, but not for RNA-binding. Interacts with RhlB, PNPase (pnp) and enolase (eno). Interacts with DeaD at reduced temperature. Associated with the cytoplasmic membrane via the N- and C-terminal regions. The N-terminal S1 motif binds RNA, and can also bind single-stranded DNA (in vitro). The C-terminal region interacts with the other degradosomal components. Essential, it cannot be deleted. In a temperature sensitive mutant at non-permissive temperature, slow processing of the 17S rRNA precursor to 16S rRNA; a double rne-rng mutated strain no longer processes the 17S rRNA precursor. In K12 strains that are derived from W1485 (including MG1655 and W3110) the rph gene has a frameshift that leads to loss of its ribonuclease PH activity. In strain K12 / MG1655(Seq)* the wild-type Rph protein has been restored (PubMed:27298395). Belongs to the RNase E/G family. RNase E subfamily.