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PR00059

Identifier
RIBOSOMALL6  [View Relations]  [View Alignment]  
Accession
PR00059
No. of Motifs
3
Creation Date
27-OCT-1994  (UPDATE 28-JUN-1999)
Title
Ribosomal protein L6 signature
Database References

PROSITE; PS00525 RIBOSOMAL_L6_1
BLOCKS; BL00525
PFAM; PF00347 Ribosomal_L6
INTERPRO; IPR000702
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).

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].
 
L6 is a protein from the large (50S) subunit; in E.coli, it is located in
the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is
known to bind directly to 23S rRNA. It belongs to a family of ribosomal
proteins, including L6 from eubacteria, cyanelles (structures that perform
similar functions to chloroplasts, but have structural and biochemical
characteristics of cyanobacteria) and mitochondria. L6 comprises 2 almost
identical folds, suggesting that is was derived by the duplication of an
ancient RNA-binding protein gene [1]. Analysis reveals several sites on the
protein surface where interactions with other ribosome components may
occur, the N-terminus being involved in protein-protein interactions and
the C-terminus containing possible RNA-binding sites [1]. 
 
RIBOSOMALL6 is a 3-element fingerprint that provides a signature for L6
ribosomal proteins. The fingerprint was derived from an initial alignment
of 5 sequences: the motifs were drawn from conserved regions spanning
virtually the full alignment length, motif 3 including the region encoded
by PROSITE pattern RIBOSOMAL_L6_1 (PS00525), a highly conserved nonapeptide
located in the putative RNA-binding region. Two iterations on OWL24.0 were
required to reach convergence, at which point a true set comprising 9
sequences was identified. Two partial matches were also found, RL6_THETH
and RM06_MARPO, both of which are fragments. Note that no archaebacterial
L6 or eukaryotic L9 proteins were detected: these are structurally and
functionally related to the L6 family identified, but lack significant
sequence similarity.
 
An update on SPTR37_9f identified a true set of 31 sequences, and 2
partial matches.
Summary Information
  31 codes involving  3 elements
2 codes involving 2 elements
Composite Feature Index
3313131
2112
123
True Positives
O23049        O67565        O84520        RK6_CYAPA     
RK6_GUITH RK6_ODOSI RK6_PORPU RL6_ACYKS
RL6_BACST RL6_BACSU RL6_BORBU RL6_CHLTR
RL6_ECOLI RL6_HAEIN RL6_HELPY RL6_MICLU
RL6_MYCCA RL6_MYCGA RL6_MYCGE RL6_MYCLE
RL6_MYCPN RL6_MYCTU RL6_STRCO RL6_SYNP6
RL6_SYNY3 RL6_THETH RL6_TREPA RM06_DICDI
RM06_PROWI RM06_RECAM RM06_YEAST
True Positive Partials
Codes involving 2 elements
RM06_MARPO RM06_SCHPO
Sequence Titles
O23049      SIMILAR TO MYCOBACTERIUM RLPF - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). 
O67565 RIBOSOMAL PROTEIN L06 - AQUIFEX AEOLICUS.
O84520 L6 RIBOSOMAL PROTEIN - CHLAMYDIA TRACHOMATIS.
RK6_CYAPA CYANELLE 50S RIBOSOMAL PROTEIN L6 - CYANOPHORA PARADOXA.
RK6_GUITH CHLOROPLAST 50S RIBOSOMAL PROTEIN L6 - GUILLARDIA THETA (CRYPTOMONAS PHI).
RK6_ODOSI CHLOROPLAST 50S RIBOSOMAL PROTEIN L6 - ODONTELLA SINENSIS.
RK6_PORPU CHLOROPLAST 50S RIBOSOMAL PROTEIN L6 - PORPHYRA PURPUREA.
RL6_ACYKS 50S RIBOSOMAL PROTEIN L6 - ACYRTHOSIPHON KONDOI SYMBIOTIC BACTERIUM.
RL6_BACST 50S RIBOSOMAL PROTEIN L6 (BL10) - BACILLUS STEAROTHERMOPHILUS.
RL6_BACSU 50S RIBOSOMAL PROTEIN L6 (BL10) - BACILLUS SUBTILIS.
RL6_BORBU 50S RIBOSOMAL PROTEIN L6 - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
RL6_CHLTR 50S RIBOSOMAL PROTEIN L6 - CHLAMYDIA TRACHOMATIS.
RL6_ECOLI 50S RIBOSOMAL PROTEIN L6 - ESCHERICHIA COLI.
RL6_HAEIN 50S RIBOSOMAL PROTEIN L6 - HAEMOPHILUS INFLUENZAE.
RL6_HELPY 50S RIBOSOMAL PROTEIN L6 - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
RL6_MICLU 50S RIBOSOMAL PROTEIN L6 - MICROCOCCUS LUTEUS (MICROCOCCUS LYSODEIKTICUS).
RL6_MYCCA 50S RIBOSOMAL PROTEIN L6 - MYCOPLASMA CAPRICOLUM.
RL6_MYCGA 50S RIBOSOMAL PROTEIN L6 - MYCOPLASMA GALLISEPTICUM.
RL6_MYCGE 50S RIBOSOMAL PROTEIN L6 - MYCOPLASMA GENITALIUM.
RL6_MYCLE 50S RIBOSOMAL PROTEIN L6 - MYCOBACTERIUM LEPRAE.
RL6_MYCPN 50S RIBOSOMAL PROTEIN L6 - MYCOPLASMA PNEUMONIAE.
RL6_MYCTU 50S RIBOSOMAL PROTEIN L6 - MYCOBACTERIUM TUBERCULOSIS.
RL6_STRCO 50S RIBOSOMAL PROTEIN L6 - STREPTOMYCES COELICOLOR.
RL6_SYNP6 50S RIBOSOMAL PROTEIN L6 - SYNECHOCOCCUS SP. (STRAIN PCC 6301).
RL6_SYNY3 50S RIBOSOMAL PROTEIN L6 - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
RL6_THETH 50S RIBOSOMAL PROTEIN L6 - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
RL6_TREPA 50S RIBOSOMAL PROTEIN L6 - TREPONEMA PALLIDUM.
RM06_DICDI MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L6 - DICTYOSTELIUM DISCOIDEUM (SLIME MOLD).
RM06_PROWI MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L6 - PROTOTHECA WICKERHAMII.
RM06_RECAM MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L6 - RECLINOMONAS AMERICANA.
RM06_YEAST 60S RIBOSOMAL PROTEIN L6, MITOCHONDRIAL PRECURSOR (YML6) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

RM06_MARPO MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L6 - MARCHANTIA POLYMORPHA (LIVERWORT).
RM06_SCHPO PUTATIVE 60S RIBOSOMAL PROTEIN L6, MITOCHONDRIAL PRECURSOR - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
Scan History
OWL24_0    2  100  NSINGLE    
OWL28_0 1 100 NSINGLE
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
LIANMVKGVHTGFEKRLEMIGVGFRA RL6_CHLTR 72 72 -
LINNHIIGVTEGHLAVLRFVGTGYRA RM06_YEAST 106 106 -
LVSNLVQGVFQGFERRLEIQGVGYRA RL6_CYAPA 71 71 -
LLANMVEGVSKGYEKALELVGVGYRA RL6_BACST 70 70 -
LLQGMLTGVSEGFKKELQITGVGYKA RL6_MYCCA 72 72 -

Motif 2 width=17
Element Seqn Id St Int Rpt
QGKKLVLSVGYSHPVEI RL6_BACST 98 2 -
DGKKLVLNIGFSHPVVI RL6_CYAPA 99 2 -
NGSKLNLSLGYSHPVEF RL6_MYCCA 100 2 -
QGSLLDLSIGVSHPTKM RL6_CHLTR 100 2 -
DGKFVNVKVGASIKQGL RM06_YEAST 136 4 -

Motif 3 width=22
Element Seqn Id St Int Rpt
VLLFAAKLRKFHPPEPYKGKGI RM06_YEAST 178 25 -
VGELAANIRAVRPPEPYKGKGI RL6_BACST 140 25 -
VGKLAAEIRAVRPPEPYKGKGI RL6_CYAPA 141 25 -
VGQVAANIRAYRKPEPYKGKGI RL6_MYCCA 142 25 -
VGEFAACVRAKRPPEPYKGKGI RL6_CHLTR 142 25 -
Final Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
LLANMVEGVSKGYEKALELVGVGYRA RL6_BACST 70 70 -
LLGNMVEGVSKGFERGLELVGVGYRA RL6_BACSU 71 71 -
IINNMVVGVTKGFEKRLELQGVGYRA RK6_GUITH 71 71 -
LVNAMVIGVTEGFTKKLVLVGVGYRA RL6_HAEIN 70 70 -
LVNNAVIGVTKGFEKKLILVGVGYRA RL6_MYCGE 74 74 -
LLQGMLTGVSEGFKKELQITGVGYKA RL6_MYCCA 72 72 -
LTDNMVVGVSKGFEKKLILVGVGYRA O23049 114 114 -
LVSNLVQGVFQGFERRLEIQGVGYRA RK6_CYAPA 71 71 -
LLNSMVIGVTEGFTKKLQLVGVGYRA RL6_ECOLI 70 70 -
LITNAIIGVTQGFEKKLRLVGVGYRA RL6_MYCPN 74 74 -
LIKNALEGVTIGFKKELRLVGVGYRA RL6_MYCGA 73 73 -
LVANMVDGVAQGFERRLEIQGVGYRA RL6_SYNY3 71 71 -
LVANLVEGVDSGFQKRLEIIGVGYRA RL6_SYNP6 71 71 -
LVKNMIKGVTEGFTEVLEIHGLGYRA O67565 75 75 -
LLNAMVVGVTEGFTKKLQLVGVGYRA RL6_ACYKS 71 71 -
LINNMVTGVSEQFQLTLNLQGVGYRA RK6_ODOSI 71 71 -
LIANMVKGVHTGFEKRLEMIGVGFRA O84520 72 72 -
LIANMVKGVHTGFEKRLEMIGVGFRA RL6_CHLTR 72 72 -
LISNMVEGVTNGFSKQLEVVGTGYRV RL6_MICLU 73 73 -
LISNMIEGVSTGFSKKLQIQGVGYRS RK6_PORPU 71 71 -
LVSNLVTGVTQGYTTKMEIFGVGYRV RL6_MYCTU 72 72 -
LVANMITGVTQGYVKKLEISGVGYRV RL6_STRCO 72 72 -
LIFNMVKGVTEGFSKSLTINGIGYRV RL6_BORBU 71 71 -
LANNIVIGLSTGFSKTLEVNGVGYKV RL6_HELPY 71 71 -
LVSNLVTGVTQGYTVSMEIFGVGYRA RL6_MYCLE 72 72 -
LIANAVKGVSEGYSKELLIKGIGYRA RL6_THETH 70 70 -
LLSNMVVGVSEGFSKTLVITGIGYRA RL6_TREPA 71 71 -
LIENMLIGVSKGYSKTIELVGVGYKA RM06_RECAM 79 79 -
LIENKFLGVSRGFCVYLEIVGVGYRA RM06_PROWI 77 77 -
LINNHIIGVTEGHLAVLRFVGTGYRA RM06_YEAST 106 106 -
TMKQQIQGVLAGFCIELKLVGLGFVV RM06_DICDI 65 65 -

Motif 2 width=17
Element Seqn Id St Int Rpt
QGKKLVLSVGYSHPVEI RL6_BACST 98 2 -
SGNKLVLNVGYSHPVEI RL6_BACSU 99 2 -
QGKDLSLSVGYSHPVVI RK6_GUITH 99 2 -
KGNAIALSLGYSHPVEH RL6_HAEIN 98 2 -
EGQFLNLQLGYSHPIKE RL6_MYCGE 102 2 -
NGSKLNLSLGYSHPVEF RL6_MYCCA 100 2 -
DGKELVLNLGFSHPVKM O23049 142 2 -
DGKKLVLNIGFSHPVVI RK6_CYAPA 99 2 -
KGNVINLSLGFSHPVDH RL6_ECOLI 98 2 -
EGETLNLQLGYSHPIKE RL6_MYCPN 102 2 -
KGNVLNLQLGYSHPINL RL6_MYCGA 101 2 -
QGNKLTLNVGYSKPVEM RL6_SYNY3 99 2 -
QGTTLILNVGYSNPVQI RL6_SYNP6 99 2 -
KGNVLELHLGKSHPDIY O67565 103 2 -
KGNVVNLALGFSHPIEH RL6_ACYKS 99 2 -
QGNSIILNLGYSHPVEL RK6_ODOSI 99 2 -
QGSLLDLSIGVSHPTKM O84520 100 2 -
QGSLLDLSIGVSHPTKM RL6_CHLTR 100 2 -
KGQDLEFDLGYSHPVPV RL6_MICLU 101 2 -
DNNNLILSVGYSHVVTI RK6_PORPU 99 2 -
KGSNLEFALGYSHPVVI RL6_MYCTU 100 2 -
KGSNLEFSLGYSHPILV RL6_STRCO 100 2 -
QGNSLFLSLGYSTQFEY RL6_BORBU 99 2 -
GNKTLDLSLGFSHPVKY RL6_HELPY 99 2 -
KGSNLEFALGYSHPVVI RL6_MYCLE 100 2 -
VGRALELTVGFSHPVVV RL6_THETH 98 2 -
QGRVLVMALGYSNDFTV RL6_TREPA 99 2 -
IDKKLVLKIGFSIEINY RM06_RECAM 107 2 -
TNDTIVLKLGHSHDIHY RM06_PROWI 116 13 -
DGKFVNVKVGASIKQGL RM06_YEAST 136 4 -
VGNTLVLDVGYSHYRSC RM06_DICDI 93 2 -

Motif 3 width=22
Element Seqn Id St Int Rpt
VGELAANIRAVRPPEPYKGKGI RL6_BACST 140 25 -
VGAIAANIRAVRSPEPYKGKGI RL6_BACSU 141 25 -
VGQIASNIRSIKPPEPYKGKGI RK6_GUITH 141 25 -
IGQVAADIRAYRRPEPYKGKGV RL6_HAEIN 140 25 -
VGQFATEIRKWRKPEPYKGKGV RL6_MYCGE 144 25 -
VGQVAANIRAYRKPEPYKGKGI RL6_MYCCA 142 25 -
IGQFAATVRKWRPPEPYKGKGV O23049 184 25 -
VGKLAAEIRAVRPPEPYKGKGI RK6_CYAPA 141 25 -
IGQVAADLRAYRRPEPYKGKGV RL6_ECOLI 140 25 -
VGQFATEVRKWRKPEPYKGKGV RL6_MYCPN 144 25 -
VGEFAIQIRKWRMPEPYKGKGV RL6_MYCGA 143 25 -
LGNTAAKIRAVRPPEPYKGKGI RL6_SYNY3 141 25 -
VGNTAARIRAVRPPEPYKGKGI RL6_SYNP6 141 25 -
VGQVAAEIRSFRKPDPYKGKGI O67565 144 24 -
IGQAAADLRAYRRPEPYKGKGV RL6_ACYKS 141 25 -
LGLFASNIRSWRPPEPYKGKGI RK6_ODOSI 141 25 -
VGEFAACVRAKRPPEPYKGKGI O84520 142 25 -
VGEFAACVRAKRPPEPYKGKGI RL6_CHLTR 142 25 -
VGETAANIRKLRRPDPYKGKGV RL6_MICLU 143 25 -
VGQVASSIRSIRPPEPYKGKGI RK6_PORPU 141 25 -
VGQIAANIRRLRRPDPYKGKGV RL6_MYCTU 142 25 -
VGEVAANIRNVRKPDPYKAKGV RL6_STRCO 142 25 -
VGQVAAEIRSLKKPEPYKGKGI RL6_BORBU 141 25 -
VGQVAAEIRSFRPPEPYKGKGV RL6_HELPY 140 24 -
VGQISANIRRLRRPDPYKGKGV RL6_MYCLE 142 25 -
VGQVAANIRAIRKPSAYHEKGI RL6_THETH 140 25 -
VGEFAAQLRRLRLPEAYKGKGI RL6_TREPA 141 25 -
VNQVAAEIRLLRKPEPYKGKGI RM06_RECAM 149 25 -
VTQVAHSIRNTRPPSVYKGKGI RM06_PROWI 158 25 -
VLLFAAKLRKFHPPEPYKGKGI RM06_YEAST 178 25 -
VTTFASLLKTFKKINMYKGTGI RM06_DICDI 134 24 -