Magnesium ions mediate contacts between phosphoryl oxygens at positions 2122 and 2176 of the 23S rRNA and ribosomal protein L1

Defect in the Formation of 70S Ribosomes Caused by Lack of Ribosomal Protein L34 Can Be Suppressed by Magnesium

“…4). It is known that the association of 30S and 50S ribosomal subunits requires Mg 2ϩ ions (25)(26)(27) and that Mg 2ϩ stabilizes the secondary structure of rRNA and the binding of the ribosomal proteins to the rRNA (28)(29)(30). These results raise the possibility that restoration of the Mg 2ϩ concentration by the disruption of yhdP and overexpression of mgtE suppresses the defect in 70S ribosome formation that is observed in the ⌬rpmH mutant.…”

“…One probable reason is stabilization of the 50S subunit. Mg 2ϩ stabilizes the binding of ribosomal proteins to the rRNA and the secondary structure of rRNA in the ribosome (28)(29)(30). Moreover, it has been demonstrated that Mg 2ϩ concentration controls the dynamics of the ribosome exquisitely through altering ribosome stability and flexibility (66).…”

“…The in vitro association of the 30S and 50S ribosomal subunits to form intact 70S ribosomes depends strongly on the concentration of Mg 2ϩ ions within the cell (25)(26)(27). Mg 2ϩ is also required for both stabilization of the secondary structure of rRNA and binding of the ribosomal proteins to the rRNA (28)(29)(30). Furthermore, Mg 2ϩ stabilizes the codon-anticodon interaction in the A site and influences the binding of ribosome recycling factor (RRF) to the ribosome (31)(32)(33)(34).…”

Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions

“…U2180 is located within a loop interconnecting H76 and H78. It has been postulated that this loop may play a critical role in the formation of an Mg 2+ binding site involved in the binding of protein L1 (14). Thus, attachment of polyamines within this region may contribute to the binding of L1 and the organization of the local conformation.…”

Staphylococcus aureus domain V functions in Escherichia coli ribosomes provided a conserved interaction with domain IV is restored

“…It is clear from numerous functional studies that domains IV and V work in concert during protein synthesis (Garrett et al+, 2000)+ Thus, it is not surprising that there would be a close structural association between these domains+ Such an association has been vividly demonstrated by the atomic level structures of the 50S subunit, where domains IV and V are visualized to be intimately associated (Ban et al+, 2000)+ What recent structures have not indicated, however, are the dynamic interactions either within or between domains+ For the 2586 region of domain V, there is functional evidence to suggest that there may be more than one interacting partner (Green et al+, 1997)+ Our studies dramatically emphasize the importance of the 1782/ 2586 partners and lend support to the notion that additional residues may be involved+ The other three potential mismatches, inferred from the 50S crystal structure, involve hydrogen bonding between residues 2358/835, 2622/2824, and 2489/ 1127+ For the first two pairs, the identity of the residue in domain V (A2358 and U2622) is actually unchanged in the hybrid; the difference lies in the nature of the paired residue (A835 in S. aureus versus C in E. coli and U2824 versus C)+ Conversely, in the third pair, the residue outside domain V is identical between E. coli and S. aureus (A1127 in domain II) but different in the peptidyl transferase center (G2489 in S. aureus versus U in E. coli )+ Thus, it is less likely that alterations in hydrogen bonding between these three less highly conserved pairs of residues would contribute to the nonfunctioning of the chimeric ribosomes+ This is the first demonstration that the substitution of a complete ribosomal domain from one organism into the rRNA of another is feasible, and opens up the possibility of establishing in a direct manner those interdomain interactions that are of functional significance+ Additionally, protein-RNA contacts can now be investigated because, despite the introduction of well over 100 altered residues, the hybrid rRNA is still recognized by the 15 or so ribosomal proteins and translation factors (e+g+, EF Tu, EF G, IF2) that interact with domain V+ Importantly, the L1 binding region of S. aureus domain V must be sufficiently recognizable that the protein can bind in a manner appropriate to initiate the assembly cascade of that part of the ribosome (Röhl & Nierhaus, 1982)+ The recognition elements crucial for protein L1 binding comprise helices 77 and 78 and some residues between them+ Mutation of residues G2123, G2125, A2126, and C2174 all reduce L1 binding (Said et al+, 1988)+ More recently, a detailed analysis of the ribose-phosphate backbone contacts with the protein have led to the proposal that helix 77 (comprising residues 2120-2124/2174-2178) binds in the cleft between the two domains of L1 (Drygin & Zimmermann, 2000)+ The residues of this helix are largely conserved between S. aureus and E. coli (Fig+ 1), presumably, therefore, preserving the recognition site for L1 in the chimera+ Unfortunately, visualizing the details of these contacts in the crystal structure is not possible as none of the protein side chain coordinates are available nor is the protein L1 binding region ordered sufficiently in the crystal for it to be modeled at atomic resolution (Ban et al+, 2000)+ Nevertheless, the atomic structure of the 50S subunit will aid in identifying nucleotide residues that can be implicated in supporting the functional interaction between domains IV and V+ Subsequent ef...…”