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PR00976

Identifier
RIBOSOMALS21  [View Relations]  [View Alignment]  
Accession
PR00976
No. of Motifs
4
Creation Date
05-OCT-1998  (UPDATE 23-JUN-1999)
Title
Ribosomal protein S21 family signature
Database References

PROSITE; PS01181 RIBOSOMAL_S21
BLOCKS; BL01181
PFAM; PF01165 Ribosomal_S21
INTERPRO; IPR001911
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).

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 S21 contains 55-70 amino acid residues, 
and has only been found in eubacteria to date. Experimental evidence has 
revealed that S21 is well exposed on the surface of the Escherichia coli 
ribosome [3], and is one of the "split proteins": these are a discrete group
that are selectively removed from 30S subunits under low salt conditions 
and are required for the formation of activated 30S reconstitution
intermediate (RI*) particles.
 
RIBOSOMALS21 is a 4-element fingerprint that provides a signature for S21
ribosomal proteins. The fingerprint was derived from an initial alignment 
of 9 sequences: the motifs were drawn from short conserved regions spanning 
the full alignment length - motifs 2 and 3 span the N-terminal region 
encoded by PROSITE pattern RIBOSOMAL_S21 (PS01181). Two iterations on
OWL30.2 were required to reach convergence, at which point a true set 
comprising 12 sequences was identified.
 
An update on SPTR37_9f identified a true set of 12 sequences, and 1
partial match.
Summary Information
  12 codes involving  4 elements
1 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
412121212
30111
20000
1234
True Positives
O51942        O67028        RS21_ANAVA    RS21_BACST    
RS21_BACSU RS21_BORBU RS21_BURPS RS21_ECOLI
RS21_HAEIN RS21_HELPY RS21_MYXXA RS21_SYNY3
True Positive Partials
Codes involving 3 elements
RS21_TREPA
Sequence Titles
O51942      30S RIBOSOMAL PROTEIN S21 - PSEUDOMONAS PUTIDA. 
O67028 RIBOSOMAL PROTEIN S21 - AQUIFEX AEOLICUS.
RS21_ANAVA 30S RIBOSOMAL PROTEIN S21 - ANABAENA VARIABILIS.
RS21_BACST 30S RIBOSOMAL PROTEIN S21 - BACILLUS STEAROTHERMOPHILUS.
RS21_BACSU 30S RIBOSOMAL PROTEIN S21 (BS-B) - BACILLUS SUBTILIS.
RS21_BORBU 30S RIBOSOMAL PROTEIN S21 - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
RS21_BURPS 30S RIBOSOMAL PROTEIN S21 - BURKHOLDERIA PSEUDOMALLAI (PSEUDOMONAS PSEUDOMALLAI).
RS21_ECOLI 30S RIBOSOMAL PROTEIN S21 - ESCHERICHIA COLI, AND SALMONELLA TYPHIMURIUM.
RS21_HAEIN 30S RIBOSOMAL PROTEIN S21 - HAEMOPHILUS INFLUENZAE.
RS21_HELPY 30S RIBOSOMAL PROTEIN S21 - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
RS21_MYXXA 30S RIBOSOMAL PROTEIN S21 - MYXOCOCCUS XANTHUS.
RS21_SYNY3 30S RIBOSOMAL PROTEIN S21 - SYNECHOCYSTIS SP. (STRAIN PCC 6803).

RS21_TREPA 30S RIBOSOMAL PROTEIN S21 - TREPONEMA PALLIDUM.
Scan History
OWL30_2    2  300  NSINGLE    
SPTR37_9f 1 100 NSINGLE
Initial Motifs
Motif 1  width=9
Element Seqn Id St Int Rpt
LLKENEPFE RS21_BURPS 5 5 -
VVGQNEPIE RS21_SYNY3 5 5 -
TVDKNENLE H70131 5 5 -
KVREGDAFD RS21_HELPY 5 5 -
KVRENESFD RS21_HAEIN 4 4 -
KVRENEPFD RS21_ECOLI 4 4 -
VVRKNESLE RS21_BACSU 4 4 -
RVKEGESIE RS21_MYXXA 5 5 -
VVGENEHIE RS21_ANAVA 5 5 -

Motif 2 width=10
Element Seqn Id St Int Rpt
ESALRRFKRQ RS21_SYNY3 13 -1 -
EKALKRFKRM H70131 13 -1 -
DVALRRFKRS RS21_HAEIN 12 -1 -
DVALRRFKRS RS21_ECOLI 12 -1 -
EDALRRFKRS RS21_BACSU 12 -1 -
ESALKRFKKA RS21_MYXXA 13 -1 -
ESALRRFKRE RS21_ANAVA 13 -1 -
EVAIRRFRRA RS21_BURPS 13 -1 -
DEAYRRFKKQ RS21_HELPY 13 -1 -

Motif 3 width=11
Element Seqn Id St Int Rpt
KEAIIREWKRR H70131 25 2 -
KAGILAEVRAR RS21_HAEIN 24 2 -
KAGVLAEVRRR RS21_ECOLI 24 2 -
KTGTLQEARKR RS21_BACSU 24 2 -
KAGILSEIRKR RS21_MYXXA 25 2 -
KAGIFQDMRKH RS21_ANAVA 25 2 -
KNGLIAELRER RS21_BURPS 25 2 -
KAGIYTDFKKH RS21_SYNY3 25 2 -
RNLVVTECRAR RS21_HELPY 25 2 -

Motif 4 width=11
Element Seqn Id St Int Rpt
FFETPQEKHKR RS21_SYNY3 37 1 -
FFESKTEKRKK RS21_HELPY 37 1 -
FYEKPTTIRKR RS21_HAEIN 36 1 -
YYEKPSTIRVK H70131 37 1 -
FYEKPTTERKR RS21_ECOLI 36 1 -
FYEKPSVKRKK RS21_BACSU 36 1 -
HYEKPSVKRKK RS21_MYXXA 37 1 -
HFETPIEKSKR RS21_ANAVA 37 1 -
AYEKPTAVRKR RS21_BURPS 37 1 -
Final Motifs
Motif 1  width=9
Element Seqn Id St Int Rpt
KVRENESFD RS21_HAEIN 4 4 -
KVRENEPFD RS21_ECOLI 4 4 -
KVKENEPFD O51942 5 5 -
VVRKNESLE RS21_BACSU 4 4 -
IVRKNESID RS21_BACST 4 4 -
RVKEGESIE RS21_MYXXA 5 5 -
VVGENEHIE RS21_ANAVA 5 5 -
LLKENEPFE RS21_BURPS 5 5 -
VVGQNEPIE RS21_SYNY3 5 5 -
TVDKNENLE RS21_BORBU 5 5 -
IVQEGEPIE O67028 5 5 -
KVREGDAFD RS21_HELPY 5 5 -

Motif 2 width=10
Element Seqn Id St Int Rpt
DVALRRFKRS RS21_HAEIN 12 -1 -
DVALRRFKRS RS21_ECOLI 12 -1 -
DVALRRFKRS O51942 13 -1 -
EDALRRFKRS RS21_BACSU 12 -1 -
DDALRRFKRA RS21_BACST 12 -1 -
ESALKRFKKA RS21_MYXXA 13 -1 -
ESALRRFKRE RS21_ANAVA 13 -1 -
EVAIRRFRRA RS21_BURPS 13 -1 -
ESALRRFKRQ RS21_SYNY3 13 -1 -
EKALKRFKRM RS21_BORBU 13 -1 -
EKVLKRFKAR O67028 13 -1 -
DEAYRRFKKQ RS21_HELPY 13 -1 -

Motif 3 width=11
Element Seqn Id St Int Rpt
KAGILAEVRAR RS21_HAEIN 24 2 -
KAGVLAEVRRR RS21_ECOLI 24 2 -
KAGVLAEVRSR O51942 25 2 -
KTGTLQEARKR RS21_BACSU 24 2 -
KTGTLQEVRKR RS21_BACST 24 2 -
KAGILSEIRKR RS21_MYXXA 25 2 -
KAGIFQDMRKH RS21_ANAVA 25 2 -
KNGLIAELRER RS21_BURPS 25 2 -
KAGIYTDFKKH RS21_SYNY3 25 2 -
KEAIIREWKRR RS21_BORBU 25 2 -
QEQILTELKRR O67028 25 2 -
RNLVVTECRAR RS21_HELPY 25 2 -

Motif 4 width=11
Element Seqn Id St Int Rpt
FYEKPTTIRKR RS21_HAEIN 36 1 -
FYEKPTTERKR RS21_ECOLI 36 1 -
FYEKPTAERKR O51942 37 1 -
FYEKPSVKRKK RS21_BACSU 36 1 -
FYEKPSVRRKK RS21_BACST 36 1 -
HYEKPSVKRKK RS21_MYXXA 37 1 -
HFETPIEKSKR RS21_ANAVA 37 1 -
AYEKPTAVRKR RS21_BURPS 37 1 -
FFETPQEKHKR RS21_SYNY3 37 1 -
YYEKPSTIRVK RS21_BORBU 37 1 -
YYEPPSERKKK O67028 37 1 -
FFESKTEKRKK RS21_HELPY 37 1 -