6Z2B

Toprim domain of RNase M5 bound with two Mg2+ ions

Summary for 6Z2B

• Entry DOI: 10.2210/pdb6z2b/pdb
• Descriptor: Ribonuclease M5, MAGNESIUM ION (3 entities in total)
• Functional Keywords: toprim domain, ribonuclease, magnesium binding, rnase m5, ribosomal rna ribonuclease, hydrolase
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 4
• Total formula weight: 50161.58

Authors

Oerum, S.,Catala, M.,Tisne, C. (deposition date: 2020-05-15, release date: 2021-03-17, Last modification date: 2024-01-24)

Primary citation

Oerum, S.,Catala, M.,Bourguet, M.,Gilet, L.,Barraud, P.,Cianferani, S.,Condon, C.,Tisne, C.
Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation.
Rna Biol., 18:1996-2006, 2021

PubMed Abstract: 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 and , the endoribonuclease (RNase) M5 performs the final step in 5S rRNA maturation, by removing the 3'- and 5'-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 Mg 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 3'-before-5' order of removal of the pre-5S rRNA extensions and map the corresponding M5 structural rearrangements during catalysis.

PubMed: 33541205
DOI: 10.1080/15476286.2021.1885896

Experimental method

X-RAY DIFFRACTION (2.138 Å)