Role of ribosomal protein L27 in peptidyl transfer

Department of Cell and Molecular Biology, Uppsala Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.
Biochemistry (Impact Factor: 3.01). 05/2008; 47(17):4898-906. DOI: 10.1021/bi8001874
Source: PubMed

ABSTRACT The current view of ribosomal peptidyl transfer is that the ribosome is a ribozyme and that ribosomal proteins are not involved in catalysis of the chemical reaction. This view is largely based on the first crystal structures of bacterial large ribosomal subunits that did not show any protein components near the peptidyl transferase center (PTC). Recent crystallographic data on the full 70S ribosome from Thermus thermophilus, however, show that ribosomal protein L27 extends with its N-terminus into the PTC in accordance with independent biochemical data, thus raising the question of whether the ribozyme picture is strictly valid. We have carried out extensive computer simulations of the peptidyl transfer reaction in the T. thermophilus ribosome to address the role of L27. The results show a reaction rate similar to that obtained in earlier simulations of the Haloarcula marismortui reaction. Furthermore, deletion of L27 is predicted to only give a minor rate reduction, in agreement with biochemical data, suggesting that the ribozyme view is indeed valid. The N-terminus of L27 is predicted to interact with the A76 phosphate group of the A-site tRNA, thereby explaining the observed impairment of A-site substrate binding for ribosomes lacking L27. Simulations are also reported for the reaction with puromycin, an A-site tRNA analogue which lacks the A76 phosphate group. The calculated energetics shows that this substrate can cause a downward p K a shift of L27 and that the reaction proceeds faster with the L27 N-terminus deprotonated, in contrast to the situation with aminoacyl-tRNA substrates. These results could explain the observed differences in pH dependence between the puromycin and C-puromycin reactions, where the former reaction has been seen to depend on an additional ionizing group besides the attacking amine, and our model predicts this ionizing group to be the N-terminal amine of L27.

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    • "It is not clear whether L27 does get cleaved, but if so, the same protease is likely responsible for the cleavage of gp46 and gp47 as well. L27 has an unusual structure with a long N-terminal extension that reaches into the peptidyl transfer site of the ribosome (Wang et al., 2004; Trobro and Aqvist, 2008), and is a target for several antibiotics (Sonenberg et al., 1973; Tejedor and Ballesta, 1986; Colca et al., 2003). It is not unlikely that the N-terminal extension in S. aureus L27 affects ribosome function and that its cleavage would be an essential process. "
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    • "The recent advances in ribosome crystallography at nearatomic resolution (Selmer et al, 2006; Laurberg et al, 2008; Weixlbaumer et al, 2008; Gao et al, 2009; Schmeing et al, 2009; Schuette et al, 2009; Voorhees et al, 2009) in combination with powerful molecular simulation techniques (Carlsson et al, 2008; Trobro and Aqvist, 2008; Wallin and Aqvist, 2010) may make such a quantitative structural analysis feasible in the near future. In fact, the power of such a combination has recently been demonstrated by the explanation (Trobro and Aqvist, 2009; Sund et al, 2010) of the accuracy of codon reading by class-1 release factors (Freistroffer et al, 2000). "
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    • "Moreover, recent crystallographic data on the full 70S ribosome from Thermus thermophilus [10] show that ribosomal protein L27 extends with its N-terminus into the PTC and makes contact with the tRNA substrates. Finally, Trobro and Aqvist have investigated the role of L27 in peptidyl transfer by carrying out computer simulations, employing the 2.8 Å T. thermophilus structure as starting coordinates [11]. "
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