1. KURLAND, C.G., JORGENSEN, F., RICHTER, A., EHRENBERG, M., BILGIN, N.
AND ROJAS, A.-M.
IN THE RIBOSOME: STRUCTURE, FUNCTION AND EVOLUTION (ED. W.E.HILL ET AL.)
PP.513-526 (AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON DC).
2. MUELLER, F. AND BRIMACOMBE, R.
A new model for the three-dimensional folding of Escherichia coli
16S ribosomal RNA. II. The RNA-protein interaction data.
J.MOL.BIOL. 271(4) 545-565 (1997).
3. MCDOUGALL, J., CHOLI, T., KRUFT, V., KAPP, U. AND WITTMANN-LIEBOLD, B.
The complete amino acid sequence of ribosomal protein S18 from
the moderate thermophile Bacillus stearothermophilus.
FEBS LETT. 245 253-260 (1989).
4. AGAFONOV, D.E., KOLB, V.A. AND SPIRIN, A.S.
Proteins on ribosome surface: measurements of protein exposure by
hot tritium bombardment technique.
PROC.NATL.ACAD.SCI.U.S.A. 94(24) 12892-7 (1997).
5. OTAKA, E., SUZUKI, K. AND HASHIMOTO, T.
Examination of protein sequence homologies. VII. The complementary molecular
coevolution of ribosomal proteins equivalent to Escherichia coli L7/L12 and
PROTEIN SEQ.DATA ANAL. 3 11-19 (1990).
Ribosomes are ribonucleoprotein particles that are the site of protein
synthesis. The structure of the ribosome is well conserved across the
prokaryotic and eukaryotic lineages, reflecting the early origin of their
essential function. They comprise two subunits, which can dissociate on
heating. In prokaryotes, the small subunit contains a single large RNA
moeity denoted, according to its sedimentation coefficient, 16S rRNA, and 21
different ribosomal proteins, designated S1-S21. Eukaryotic small ribosomal
subunits contain 33 proteins, many of which are similar to those found
There are two major tRNA binding sites on the ribosome, termed the A site,
where incoming aminoacyl-tRNA is bound, and the P site (for peptidyl tRNA),
where new peptide bonds are formed. The ribosomal proteins catalyse ribosome
assembly and stabilise the rRNA, tuning the structure of the ribosome for
optimal function . Evidence suggests that, in prokaryotes, the peptidyl
transferase reaction is performed by the large subunit 23S rRNA, whereas
proteins probably have a greater role in eukaryotic ribosomes. Most of the
proteins lie close to, or on the surface of, the 30S subunit, arranged
peripherally around the rRNA . The small subunit ribosomal proteins can
be categorised as primary binding proteins, which bind directly and
independently to 16S rRNA; secondary binding proteins, which display no
specific affinity for 16S rRNA, but its assembly is contingent upon the
presence of one or more primary binding proteins; and tertiary binding
proteins, which require the presence of one or more secondary binding
proteins and sometimes other tertiary binding proteins.
The small ribosomal subunit protein S18 is known to be involved in binding
the aminoacyl-tRNA complex in E.coli , and appears to be situated at the
tRNA A-site. Experimental evidence has revealed that S18 is well exposed
on the surface of the E.coli ribosome, and is a secondary rRNA binding
protein . S18 belongs to a family of ribosomal proteins  that includes:
eubacterial S18; algal and plant chloroplast S18; and cyanelle S18.
RIBOSOMALS18 is a 4-element fingerprint that provides a signature for S18
ribosomal proteins. The fingerprint was derived from an initial alignment
of 14 sequences: the motifs were drawn from short conserved regions spanning
the full alignment length - motifs 2 and 3 span the region encoded by
PROSITE pattern RIBOSOMAL_S18 (PS00057), which contains two basic residues
that may be involved in RNA-binding. Two iterations on OWL30.2 were required
to reach convergence, at which point a true set comprising 29 sequences was
identified. A single partial match was also found, AE0006723, a gene product
from the hyperthermophilic bacterium Aquifex aeolicus that fails to make a
significant match with motif 2.
An update on SPTR37_9f identified a true set of 33 sequences, and 1