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PR00972

Identifier
RIBSOMALS12E  [View Relations]  [View Alignment]  
Accession
PR00972
No. of Motifs
4
Creation Date
05-OCT-1998  (UPDATE 04-JUL-1999)
Title
Ribosomal protein S12E family signature
Database References

PROSITE; PS01189 RIBOSOMAL_S12E
BLOCKS; BL01189
PFAM; PF01164 Ribosomal_S12e
INTERPRO; IPR000530
Literature References
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. 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).
 
4. LIN, A., CHAN, Y.-L., JONES, R. AND WOOL, I.G.
The primary structure of rat ribosomal protein S12. The relationship of
rat S12 to other ribosomal proteins and a correlation of the amino acid
sequences of rat and yeast ribosomal proteins.
J.BIOL.CHEM. 262 14343-14351 (1987).
 
5. MARCHAL, C., ISMAILI, N. AND PAYS, E.
A ribosomal S12-like gene of Trypanosoma brucei.
MOL.BIOCHEM.PARASITOL. 57 331-334 (1993).

Documentation
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
in prokaryotes. 
 
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 [1]. 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 [2]. 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 S12 contains 130-150 amino acid residues,
and is thought to be involved in the translation initiation step. Eukaryotic 
S12 ribosomal proteins include: vertebrate S12 [4]; Trypanosoma brucei S12
[5]; Caenorhabditis elegans S12 (F54E7.2); Drosophila S12; and yeast S12.
 
RIBSOMALS12E is a 4-element fingerprint that provides a signature for 
eukaryotic S12 ribosomal proteins. The fingerprint was derived from an
initial alignment of 8 sequences: the motifs were drawn from short conserved 
regions spanning the full alignment length - motif 1 includes most of the
N-terminal region encoded by PROSITE pattern RIBOSOMAL_S12E (PS01189). Two
iterations on OWL30.2 were required to reach convergence, at which point a
true set comprising 12 sequences was identified. A single partial match was
also found, RS6X_SULSO, a member of the L7AE family of ribosomal proteins 
that matches motifs 2 and 3.
 
An update on SPTR37_9f identified a true set of 11 sequences, and 4
partial matches.
Summary Information
  11 codes involving  4 elements
1 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
411111111
31101
20110
1234
True Positives
O59936        O74322        RS12_CAEEL    RS12_HUMAN    
RS12_ORENI RS12_PIG RS12_RAT RS12_SCHPO
RS12_TRYBB RS12_XENLA RS12_YEAST
True Positive Partials
Codes involving 3 elements
O76223
Codes involving 2 elements
RS6X_SULSO
Sequence Titles
O59936      40S RIBOSOMAL PROTEIN S12 - ERYSIPHE GRAMINIS (SUBSP. HORDEI) (GRASS MILDEW). 
O74322 40S RIBOSOMAL PROTEIN S12 TYPE - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
RS12_CAEEL PROBABLE 40S RIBOSOMAL PROTEIN S12 - CAENORHABDITIS ELEGANS.
RS12_HUMAN 40S RIBOSOMAL PROTEIN S12 - HOMO SAPIENS (HUMAN).
RS12_ORENI 40S RIBOSOMAL PROTEIN S12 - OREOCHROMIS NILOTICUS (NILE TILAPIA) (TILAPIA NILOTICA).
RS12_PIG 40S RIBOSOMAL PROTEIN S12 - SUS SCROFA (PIG).
RS12_RAT 40S RIBOSOMAL PROTEIN S12 - MUS MUSCULUS (MOUSE), AND RATTUS NORVEGICUS (RAT).
RS12_SCHPO 40S RIBOSOMAL PROTEIN S12 - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
RS12_TRYBB 40S RIBOSOMAL PROTEIN S12 - TRYPANOSOMA BRUCEI BRUCEI.
RS12_XENLA 40S RIBOSOMAL PROTEIN S12 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
RS12_YEAST 40S RIBOSOMAL PROTEIN S12 - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

O76223 RIBOSOMAL PROTEIN S12 - TRYPANOSOMA BRUCEI BRUCEI.

RS6X_SULSO 30S RIBOSOMAL PROTEIN HS6-LIKE - SULFOLOBUS SOLFATARICUS.
Scan History
OWL30_2    2  300  NSINGLE    
SPTR37_9f 1 100 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
VLRTALVHDGLARG RS12_YEAST 31 31 -
VLRAAHHADGLAKG RS12_CAEEL 34 34 -
VLKKSLIADGLVHG RS12_DROME 40 40 -
VLMKARETNGLICG RS12_TRYBB 35 35 -
VLKTALIHDGLARG RS12_HUMAN 20 20 -
VLKTALIHDGLARG RS12_XENLA 20 20 -
VLKTALIHDGLARG RS12_RAT 20 20 -
VLKTALIHDGLARG RS12_PIG 20 20 -

Motif 2 width=17
Element Seqn Id St Int Rpt
LHETCKALDKREAHFCV RS12_CAEEL 48 0 -
IHQACKALDKRQAVLCI RS12_DROME 54 0 -
IREAAKALDKRQAHLCV RS12_HUMAN 34 0 -
IREAAKALDKRQAHLCV RS12_XENLA 34 0 -
IREAAKALDKRQAHLCV RS12_RAT 34 0 -
IREAAKALDKRQAHLCV RS12_PIG 34 0 -
LRESTKALTRGEALLVV RS12_YEAST 45 0 -
LSEVTRALDRRTAHLCV RS12_TRYBB 49 0 -

Motif 3 width=22
Element Seqn Id St Int Rpt
LIRVDSHKKLGEWSGLCKIDKE RS12_DROME 95 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_HUMAN 75 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_XENLA 75 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_RAT 75 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_PIG 75 24 -
LIKVADAKQLGEWAGLGKIDRE RS12_YEAST 88 26 -
LIKVADKKIIGEYCGLCKYDKE RS12_CAEEL 89 24 -
LVSMDEREKLAQWAGLTRMAAD RS12_TRYBB 90 24 -

Motif 4 width=14
Element Seqn Id St Int Rpt
RKVVGCSSAVVTNW RS12_CAEEL 114 3 -
RKTLKCSCLAVRDF RS12_TRYBB 115 3 -
RKVVGCSCVVVKDY RS12_HUMAN 100 3 -
RKVCGCSVVVIKDF RS12_DROME 120 3 -
RKVVGCSCVVVKDY RS12_XENLA 100 3 -
RKVVGCSCVVVKDY RS12_RAT 100 3 -
RKVVGCSCVVVKDY RS12_PIG 100 3 -
RKVVGASVVVVKNW RS12_YEAST 113 3 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
VLKTALIHDGLARG RS12_HUMAN 20 20 -
VLKTALIHDGLARG RS12_XENLA 20 20 -
VLKTALIHDGLARG RS12_RAT 20 20 -
VLKTALIHDGLARG RS12_PIG 20 20 -
VLKTALIHDGLAPG RS12_ORENI 20 20 -
VLKRALVHDGLARG RS12_SCHPO 36 36 -
VLKRALVHDGLARG O74322 39 39 -
VLRTALVHDGLARG RS12_YEAST 31 31 -
ALRTALMHDGLARG O59936 21 21 -
VLRAAHHADGLAKG RS12_CAEEL 34 34 -
VLMKARETNGLICG RS12_TRYBB 35 35 -

Motif 2 width=17
Element Seqn Id St Int Rpt
IREAAKALDKRQAHLCV RS12_HUMAN 34 0 -
IREAAKALDKRQAHLCV RS12_XENLA 34 0 -
IREAAKALDKRQAHLCV RS12_RAT 34 0 -
IREAAKALDKRQAHLCV RS12_PIG 34 0 -
IREAAKALDKRQAHLCV RS12_ORENI 34 0 -
IREASKALDRRQAHLCV RS12_SCHPO 50 0 -
IREASKALDRRQAHLCV O74322 53 0 -
LRESTKALTRGEALLVV RS12_YEAST 45 0 -
LREASKALDRREAHMCV O59936 35 0 -
LHETCKALDKREAHFCV RS12_CAEEL 48 0 -
LSEVTRALDRRTAHLCV RS12_TRYBB 49 0 -

Motif 3 width=22
Element Seqn Id St Int Rpt
LIKVDDNKKLGEWVGLCKIDRE RS12_HUMAN 75 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_XENLA 75 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_RAT 75 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_PIG 75 24 -
LIKVDDNKKLGEWVGLCKIDRE RS12_ORENI 75 24 -
LIKVADPKVLGEWAGLCVLDRD RS12_SCHPO 91 24 -
LVKVADPKILGEWAGLCVLDRD O74322 94 24 -
LIKVADAKQLGEWAGLGKIDRE RS12_YEAST 88 26 -
LIKVPDGKQLGEWAGLCVLDRE O59936 76 24 -
LIKVADKKIIGEYCGLCKYDKE RS12_CAEEL 89 24 -
LVSMDEREKLAQWAGLTRMAAD RS12_TRYBB 90 24 -

Motif 4 width=14
Element Seqn Id St Int Rpt
RKVVGCSCVVVKDY RS12_HUMAN 100 3 -
RKVVGCSCVVVKDY RS12_XENLA 100 3 -
RKVVGCSCVVVKDY RS12_RAT 100 3 -
RKVVGCSCVVVKDY RS12_PIG 100 3 -
RKVVGCSCVVVKDY RS12_ORENI 100 3 -
RKVVGCSCVAVTDY RS12_SCHPO 116 3 -
RKVVGCSCVAVTDY O74322 119 3 -
RKVVGASVVVVKNW RS12_YEAST 113 3 -
RKVVNCSCVVVKNW O59936 101 3 -
RKVVGCSSAVVTNW RS12_CAEEL 114 3 -
RKTLKCSCLAVRDF RS12_TRYBB 115 3 -