Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation

All species transcribe ribosomal RNA in an immature form that requires several enzymes for processing into mature rRNA. The number and types of enzymes utilized for these processes vary greatly between different species. In low G + C Gram-positive bacteria including Bacillus subtilis and Geobacillus stearothermophilus, the endoribonuclease (RNase) M5 performs the final step in 5S rRNA maturation, by removing the 3MODIFIER LETTER PRIME- and 5MODIFIER LETTER PRIME-extensions from precursor (pre) 5S rRNA. This cleavage activity requires initial complex formation between the pre-rRNA and a ribosomal protein, uL18, making the full M5 substrate a ribonucleoprotein particle (RNP). M5 contains a catalytic N-terminal Toprim domain and an RNA-binding C-terminal domain, respectively, shown to assist in processing and binding of the RNP. Here, we present structural data that show how two Mg2+ ions are accommodated in the active site pocket of the catalytic Toprim domain and investigate the importance of these ions for catalysis. We further perform solution studies that support the previously proposed 3MODIFIER LETTER PRIME-before-5MODIFIER LETTER PRIME order of removal of the pre-5S rRNA extensions and map the corresponding M5 structural rearrangements during catalysis.

Automated summary

The NRase M5 enzyme plays a crucial role in the maturation of 5S rRNA in low G + C Gram-positive bacteria, by forming a complex with ribosomal protein uL18. Structural data reveals the accommodation of two Mg2+ ions in the active site pocket of the catalytic Toprim domain of M5 and their importance for catalysis. Solution studies support the proposed 3'-5' order of removal of pre-5S rRNA extensions and show the corresponding M5 structural rearrangements during catalysis.