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 stearothermophilus
has been determined at 1.8 Å resolution. The molecule
consists of a five-stranded antiparallel β-sheet and
four α-helices, which fold in a way that is topologically
similar to the ribonucleoprotein (RNP) domain. The molecular
shape and electrostatic representation suggest that the
concave surface and loop regions are involved in 5S rRNA
binding. To identify amino acid residues responsible for
5S rRNA binding, we made use of Ala-scanning mutagenesis
of evolutionarily conserved amino acids occurring in the
β-strands and loop regions. The mutations of Asn37
at the β1-strand and Gln63 at the loop between helix
2 and β3-strand as well as that of Phe77 at the tip
of the loop structure between the β2- and β3-strands
caused a significant reduction in 5S rRNA binding. In addition,
the mutations of Thr90 on the β3-strand and Ile141
and Asp144 at the loop between β4- and β5-strands
moderately reduced the 5S rRNA-binding affinity. Comparison
of these results with the more recently analyzed structure
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.