Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins

Abstract

The crystal structure of Thermus thermophilus ribosomal protein TL5 in complex with a fragment of Escherichia coli 5S rRNA has been determined at 2.3 A resolution. The protein consists of two domains. The structure of the N-terminal domain is close to the structure of E. coli ribosomal protein L25, but the C-terminal domain represents a new fold composed of seven beta-strands connected by long loops. TL5 binds to the RNA through its N-terminal domain, whereas the C-terminal domain is not included in this interaction. Cd(2+) ions, the presence of which improved the crystal quality significantly, bind only to the protein component of the complex and stabilize the protein molecule itself and the interactions between the two molecules in the asymmetric unit of the crystal. The TL5 sequence reveals homology to the so-called general stress protein CTC. The hydrophobic cores which stabilize both TL5 domains are highly conserved in CTC proteins. Thus, all CTC proteins may fold with a topology close to that of TL5.

Functional aspects of ribosomal architecture: symmetry, chirality and regulation

“…The three CTC domains are shown. Domain-1 (red) resembles protein L25; 67 domain-2 (green), which together with domain 1 forms a structure almost identical to that of protein TL5, 68 and domain-3 (gold), which is unique to D. radiodurans. 7 Highlighted are the approximate locations of the B1a intersubunit bridge (also known as the 'A-site finger' or helix H38) and of the acceptor stem of the A-site tRNA (in violet and blue, respectively).…”

“…2 The fold of a hypothetical D50S protein, built from the CTC N-terminal and middle domains is almost identical to the fold of the two-domain protein TL5 from T. thermophilus. 68 The slight changes in the relative orientations of the two domains in the two proteins can be correlated with crystal vs ribosome environments. Hence, it seems that TL5 occupies the same position, namely wraps around a B1a bridge, in the T. thermophilus ribosome.…”

A Bright Future for Antibiotics?

“…The C-terminal domain (also known as domain 1) is homologous to protein L25 in E. coli, namely the 5S rRNA-binding protein. Domains 1 + 2 (namely the C-terminal + the middle domains) are homologous to protein TL5 in the T. thermophilus ribosome (124). Domain 3 (the N-terminal domain) is bound to the middle domain (domain 2) by a single strand, presumably facilitating the extreme (unusual) flexibility in its position within the ribosome, as indicated by the lower quality of its electron density map.…”

Cyclic di-AMP: another second messenger enters the fray

“…The structures of two of the four YbbR domain--containing proteins from Desulfitobacterium hafniense Y51 have been solved by NMR and X--ray crystallography 26 . It was noted that the YbbR domains assume a similar fold to the C--terminal domain of the ribosomal proteins TL5 from Thermus thermophilus and L25 from Deinococcus radiodurans 27,28 . It has been suggested that this domain serves to stabilize the interaction between the 5S rRNA, to which these proteins bind, and the 23S rRNA via an interaction with the 23S rRNA--binding ribosomal protein L16 26 , highlighting that a protein with a similar fold to YbbR can bind both RNA and proteins.…”