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PR00064

Identifier
RIBOSOMALL35  [View Relations]  [View Alignment]  
Accession
PR00064
No. of Motifs
3
Creation Date
28-OCT-1994  (UPDATE 29-JUL-1999)
Title
Ribosomal protein L35 signature
Database References

PROSITE; PS00936 RIBOSOMAL_L35
INTERPRO; IPR001706
Literature References
1. GOLDEN, B.L., RAMAKRISHNAN, V. AND WHITE, S.W.
Ribosomal protein L: structural evidence of gene duplication from a 
primitive RNA binding protein.
EMBO J. 12 4901-4908 (1993).
 
2. RAMAKRISHNAN, V. AND GERCHMAN, S.E.
Cloning, sequencing, and overexpression of genes for ribosomal proteins 
from Bacillus stearothermophilus.
J.BIOL.CHEM. 266 880-885 (1991).
 
3. KASHIWAGI, K. AND IGARASHI, K.
Nonspecific inhibition of Escherichia coli ornithine decarboxylase by
various ribosomal proteins: detection of a new ribosomal protein possessing
strong antizyme activity.
BIOCHIM.BIOPHYS.ACTA 911 180-190 (1987).
 
4. SMOOKER, P.M., CHOLI, T. AND SUBRAMANIAN, A.R.
Ribosomal protein L35: identification in spinach chloroplasts and isolation
of a cDNA clone encoding its cytoplasmic precursor.
BIOCHEMISTRY 29 9733-9736 (1990).

Documentation
Protein synthesis is co-ordinated in all cells by ribosomes, ribonucleo-
protein particles containing more than 50 different proteins and several
large RNAs [1]. Low resolution models show the protein arrangement in both
the large and small ribosomal subunits, but higher resolution structures are
required to reveal the detailed mechanistic functioning of the complex [2].
 
L35 is a basic protein from the large (50S) subunit [3]. Like many
basic polypeptides, L35 completely inhibits ornithine decarboxylase when
present unbound in the cell, but the inhibitory function is abolished upon 
its incorporation into ribosomes [3]. It belongs to a family of ribosomal
proteins, including L35 from eubacteria, plants and cyanelles - in lower
plants it is found in the chloroplast, but is located in the nucleus in
higher plants, suggesting chloroplast-to-nucleus relocation during the
evolution of higher plants [4].
 
RIBOSOMALL35 is a 3-element fingerprint that provides a signature for L35
ribosomal proteins. The fingerprint was derived from an initial alignment
of 5 sequences: the motifs were drawn from conserved regions spanning the
full alignment length, motif 1 including the N-terminal region encoded by
PROSITE pattern RIBOSOMAL_l35 (PS00936). Two iterations on OWL24.0 were
required to reach convergence, at which point a true set comprising 6
sequences was identified.
 
An update on SPTR37_9f identified a true set of 21 sequences, and 3
partial matches.
Summary Information
  21 codes involving  3 elements
3 codes involving 2 elements
Composite Feature Index
3212121
2132
123
True Positives
O66982        O68845        O82237        O84841        
O88059 P94976 RK35_CYAPA RK35_GUITH
RK35_ODOSI RK35_PORPU RK35_SPIOL RL35_BACST
RL35_BACSU RL35_BORBU RL35_BUCAP RL35_ECOLI
RL35_HAEIN RL35_MYCFE RL35_PSESY RL35_SYNY3
RL35_TREPA
True Positive Partials
Codes involving 2 elements
RL35_HELPY RL35_MYCGE RL35_MYCPN
Sequence Titles
O66982      50S RIBOSOMAL PROTEIN L35 - AQUIFEX AEOLICUS. 
O68845 RIBOSOMAL PROTEIN L35 - VIBRIO CHOLERAE.
O82237 50S RIBOSOMAL PROTEIN L35 - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O84841 L35 RIBOSOMAL PROTEIN - CHLAMYDIA TRACHOMATIS.
O88059 50S RIBOSOMAL PROTEIN L35 - STREPTOMYCES COELICOLOR.
P94976 RPMI - MYCOBACTERIUM TUBERCULOSIS.
RK35_CYAPA CYANELLE 50S RIBOSOMAL PROTEIN L35 - CYANOPHORA PARADOXA.
RK35_GUITH CHLOROPLAST 50S RIBOSOMAL PROTEIN L35 - GUILLARDIA THETA (CRYPTOMONAS PHI).
RK35_ODOSI CHLOROPLAST 50S RIBOSOMAL PROTEIN L35 - ODONTELLA SINENSIS.
RK35_PORPU CHLOROPLAST 50S RIBOSOMAL PROTEIN L35 - PORPHYRA PURPUREA.
RK35_SPIOL 50S RIBOSOMAL PROTEIN L35, CHLOROPLAST PRECURSOR (CL35) - SPINACIA OLERACEA (SPINACH).
RL35_BACST 50S RIBOSOMAL PROTEIN L35 - BACILLUS STEAROTHERMOPHILUS.
RL35_BACSU 50S RIBOSOMAL PROTEIN L35 - BACILLUS SUBTILIS.
RL35_BORBU 50S RIBOSOMAL PROTEIN L35 - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
RL35_BUCAP 50S RIBOSOMAL PROTEIN L35 - BUCHNERA APHIDICOLA.
RL35_ECOLI 50S RIBOSOMAL PROTEIN L35 (RIBOSOMAL PROTEIN A) - ESCHERICHIA COLI.
RL35_HAEIN 50S RIBOSOMAL PROTEIN L35 - HAEMOPHILUS INFLUENZAE.
RL35_MYCFE 50S RIBOSOMAL PROTEIN L35 - MYCOPLASMA FERMENTANS.
RL35_PSESY 50S RIBOSOMAL PROTEIN L35 - PSEUDOMONAS SYRINGAE (PV. SYRINGAE).
RL35_SYNY3 50S RIBOSOMAL PROTEIN L35 - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
RL35_TREPA 50S RIBOSOMAL PROTEIN L35 - TREPONEMA PALLIDUM.

RL35_HELPY 50S RIBOSOMAL PROTEIN L35 - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
RL35_MYCGE 50S RIBOSOMAL PROTEIN L35 - MYCOPLASMA GENITALIUM.
RL35_MYCPN 50S RIBOSOMAL PROTEIN L35 - MYCOPLASMA PNEUMONIAE.
Scan History
OWL24_0    2  100  NSINGLE    
SPTR37_9f 3 50 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
KMKTHKASAKRFRVTGKG RL35_SPIOL 91 91 -
KLKTRKAAAKRYKAVGNK RL35_CYAPA 3 3 -
KIKTVRGASKRFKKTGKG RL35_ECOLI 2 2 -
KMKTHRGSAKRFKKTASG RL35_BACST 2 2 -
KMKTKSALKKRIKITGTG RL35_MYCFE 3 3 -

Motif 2 width=15
Element Seqn Id St Int Rpt
KLKRGHAYTSHLFAN RL35_BACST 20 0 -
KIMREQAYRSHLSQN RL35_MYCFE 21 0 -
KIVRRRAGKQHLLAK RL35_SPIOL 109 0 -
KISRRKAFRSHLLQK RL35_CYAPA 21 0 -
GFKHKHANLRHILTK RL35_ECOLI 20 0 -

Motif 3 width=19
Element Seqn Id St Int Rpt
KNTKRKNRLSKLIQVDRSD RL35_SPIOL 124 0 -
KATKRKRHLRPKAMVSKGD RL35_ECOLI 35 0 -
KTKKQKRHLRKATLVSPGD RL35_BACST 35 0 -
KTTKQKRQARKSVQMHSSD RL35_MYCFE 36 0 -
KSTNRKRQLSQVVIASPGD RL35_CYAPA 36 0 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
KIKTLRSAAKRFKKTASG RL35_BUCAP 3 3 -
KIKTVRGASKRFKKTGKG RL35_ECOLI 2 2 -
KIKTVRGAAKRFKKTASG RL35_HAEIN 2 2 -
KMKTHRGSAKRFKKTGSG RL35_BACSU 2 2 -
KMKTHKASAKRFRVTGKG RK35_SPIOL 91 91 -
KMKTHRGSAKRFKKTASG RL35_BACST 2 2 -
KMKTKSGAAKRFLKTANG RL35_PSESY 3 3 -
KLKTRKSARKRFYISAKG RK35_GUITH 3 3 -
KLKTRKAALKRYKKTATG RK35_ODOSI 3 3 -
KMKTNRSAAKRFKVTAKG O66982 5 5 -
KMKTKSAAAKRFSVTGAG RL35_TREPA 3 3 -
KLKTRKAAAKRYKAVGNK RK35_CYAPA 3 3 -
KLKTSKAIAKRFKVSSSG RK35_PORPU 3 3 -
KMKNNKGAAKRFKKTAGG O68845 3 3 -
KMKTRKSAKKRYSFTVNG RL35_BORBU 4 4 -
KMKTHKASAKRFRVTGRG O82237 76 76 -
KLKTRKAAAKRFRPTGSG RL35_SYNY3 3 3 -
KAKTHSGASKRFRRTGTG P94976 3 3 -
KNKSHSGASKRFKITGSG O88059 3 3 -
KMKTKSALKKRIKITGTG RL35_MYCFE 3 3 -
KMKSNKSVAARFKLTGSG O84841 3 3 -

Motif 2 width=15
Element Seqn Id St Int Rpt
KFKRKQANLRHILTK RL35_BUCAP 21 0 -
GFKHKHANLRHILTK RL35_ECOLI 20 0 -
GFKRKQSHLRHILTK RL35_HAEIN 20 0 -
KLKRSHAYTSHLFAN RL35_BACSU 20 0 -
KIVRRRAGKQHLLAK RK35_SPIOL 109 0 -
KLKRGHAYTSHLFAN RL35_BACST 20 0 -
GIKHKHAFKSHILTK RL35_PSESY 20 -1 -
KFVRKRAFKSHILEK RK35_GUITH 21 0 -
KFLRRHAYKGHLLMK RK35_ODOSI 21 0 -
KIKRWKSGGAHYNTK O66982 23 0 -
KVKFKKMNLRHILTK RL35_TREPA 21 0 -
KISRRKAFRSHLLQK RK35_CYAPA 21 0 -
KILRHKASKSHLLQK RK35_PORPU 21 0 -
GIKYKHATKRHILTK O68845 20 -1 -
KVKYKKQNLRHILTK RL35_BORBU 22 0 -
KIVRRRSGKQHLLAK O82237 94 0 -
KIIRRKAFKNHLLEH RL35_SYNY3 22 1 -
KIVRQKANRRHLLEH P94976 21 0 -
KVLRERAGKRHLLEH O88059 21 0 -
KIMREQAYRSHLSQN RL35_MYCFE 21 0 -
QLKRTRPGKRHKLSK O84841 21 0 -

Motif 3 width=19
Element Seqn Id St Int Rpt
KTTTKKRHLRPKILVSKGD RL35_BUCAP 36 0 -
KATKRKRHLRPKAMVSKGD RL35_ECOLI 35 0 -
KTTKRKRHLRHKSMVAKAD RL35_HAEIN 35 0 -
KSQKQKRKLRKSAVVSAGD RL35_BACSU 35 0 -
KNTKRKNRLSKLIQVDRSD RK35_SPIOL 124 0 -
KTKKQKRHLRKATLVSPGD RL35_BACST 35 0 -
MSTKRKRQLRGSSLLHPSD RL35_PSESY 35 0 -
KTSKRKRNLKRKMIVFKGE RK35_GUITH 36 0 -
KSKTQKRKLSQIICVSNND RK35_ODOSI 36 0 -
KSSKRKRHLRKHTYVKDNM O66982 38 0 -
KAPKRKRKLRHAGFLSKVE RL35_TREPA 36 0 -
KSTNRKRQLSQVVIASPGD RK35_CYAPA 36 0 -
KSSKHRRHLSSTCQVDSRD RK35_PORPU 36 0 -
RTTKNKRQLRPNAILPKCE O68845 35 0 -
KSSKRKRNLRKSGNLSCFE RL35_BORBU 37 0 -
KNNKRKLRLSKMVHGSEPE O82237 109 0 -
SSEQKHRRLSNLALVHEAD RL35_SYNY3 38 1 -
KPSTRTRRLDGRTVVAAND P94976 36 0 -
KSSRVTRRLTGNAEMAPGD O88059 36 0 -
KTTKQKRQARKSVQMHSSD RL35_MYCFE 36 0 -
RSSQQKRNLSKQPLVDQGQ O84841 36 0 -