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PROSITE documentation PDOC00454

Ribosomal protein L6 signatures

Description:

Ribosomal protein L6 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L6 is known to bind directly to the 23S rRNA and is located at the aminoacyl-tRNA binding site of the peptidyltransferase center. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [1,2,3,4], groups:

  • Eubacterial L6.
  • Algal chloroplast L6.
  • Cyanelle L6.
  • Archaebacterial L6.
  • Marchantia polymorpha mitochondrial L6.
  • Yeast mitochondrial YmL6 (gene MRPL6).
  • Mammalian L9.
  • Drosophila L9.
  • Plants L9.
  • Yeast L9 (YL11).

While all the above proteins are evolutionary related it is very difficult to derive a pattern that will find them all. We therefore decided to create two patterns, the first to detect eubacterial, cyanelle and mitochondrial L6, the second to detect archaebacterial L6 as well as eukaryotic L9.

Last update:

December 2004 / Pattern and text revised.

Technical section:

PROSITE methods (with tools and information) covered by this documentation:

RIBOSOMAL_L6_1, PS00525; Ribosomal protein L6 signature 1  (PATTERN)
Consensus pattern: [PS]-[DENS]-x-Y-K-[GA]-K-G-[LIVM]
Sequences known to belong to this class detected by the pattern: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00525
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00525
• Scan Swiss-Prot/TrEMBL entries against PS00525
• view ligand binding statistics
Matching PDB structures: 1EG0 1GIY 1P85 1P86 ... [ALL]
RIBOSOMAL_L6_2, PS00700; Ribosomal protein L6 signature 2  (PATTERN)
Consensus pattern: [QLS]-x(3)-[LIVM]-x(2)-[KRWYF]-x(2)-R-x-F-x-D-G-[LIVM]-[YF]-[LIVM]-x(2)-[KR]
Sequences known to belong to this class detected by the pattern: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00700
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00700
• Scan Swiss-Prot/TrEMBL entries against PS00700
• view ligand binding statistics
Matching PDB structures: 1FFK 1JJ2 1K5Y 1K73 ... [ALL]

References:

1 AuthorsSuzuki K., Olvera J., Wool I.G.
TitleThe primary structure of rat ribosomal protein L9.
SourceGene 93:297-300(1990).
PubMed ID2227441
2 AuthorsHarrer R., Schwank S., Schueller H.-J., Schweizer E.
TitleMolecular cloning and analysis of the nuclear gene MRP-L6 coding for a putative mitochondrial ribosomal protein from Saccharomyces cerevisiae.
SourceCurr. Genet. 24:136-140(1993).
PubMed ID8358820
3 AuthorsGolden B.L., Ramakrishnan V., White S.W.
TitleRibosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein.
SourceEMBO J. 12:4901-4908(1993).
PubMed ID8262035
4 AuthorsOtaka E., Hashimoto T., Mizuta K., Suzuki K.
SourceProtein Seq. Data Anal. 5:301-313(1993).

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