T. Nakashima et al., Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding, RNA, 7(5), 2001, pp. 692-701
Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and
plays an essential role in the promotion of a particular conformation of 5S
rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stea
rothermophilus has been determined at 1.8 Angstrom resolution. The molecule
consists of a five-stranded antiparallel beta -sheet and four alpha -helic
es, which fold in a way that is topologically similar to the ribonucleoprot
ein (RNP) domain. The molecular shape and electrostatic representation sugg
est that the concave surface and loop regions are involved in 5S rRNA bindi
ng. To identify amino acid residues responsible for 5S rRNA binding, we mad
e use of Ala-scanning mutagenesis of evolutionarily conserved amino acids o
ccurring in the beta -strands and loop regions. The mutations of Asn37 at t
he beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as w
ell as that of Phe77 at the tip of the loop structure between the beta2- an
d beta3-strands caused a significant reduction in 5S rRNA binding. In addit
ion, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at th
e loop between beta4- and beta5-strands moderately reduced the 5S rRNA-bind
ing affinity. Comparison of these results with the more recently analyzed s
tructure of the 50S subunit from Haloarcula marismortui suggests that there
are significant differences in the structure at N- and C-terminal regions
and probably in the 5S rRNA binding.