Small protein B (SmpB) superfamily
|General category ||Other|
|Detailed category ||Unknown function|
Document: Function annotation of SCOP domain superfamilies
UniProtKB KeyWords (KW)(show details)
Highlighted in gray are those with FDR_all>0.001
Document: KW annotation of SCOP domains
|Cross references ||IPR000037 SSF74982 Protein matches|
|Abstract ||In bacteria, SsrA RNA recognises ribosomes stalled on defective messages and acts as a tRNA and mRNA to mediate
the addition of a short peptide tag to the C-terminus of the partially synthesized nascent polypeptide chain. The
SsrA-tagged protein is then degraded by C-terminal-specific proteases. |
SmpB, a unique RNA-binding protein that is
conserved throughout the bacterial kingdom is an essential component of the SsrA quality-control
system. Deletion of the smpB gene in Escherichia coli results in the same phenotypes observed in ssrA-defective cells,
including a variety of phage development defects and the failure to tag proteins translated from defective mRNAs. Purified
SmpB binds specifically and with high affinity to SsrA RNA and is required for stable association of SsrA with ribosomes
in vivo. Formation of an SmpB-SsrA complex appears to be critical in mediating SsrA activity after aminoacylation with
alanine but prior to the transpeptidation reaction that couples this alanine to the nascent chain. SsrA RNA is present at
wild-type levels in the smpB mutant arguing against a model of SsrA action that involves direct competition for
transcription factors .
PDBeMotif information about ligands, sequence and structure motifs
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Internal database links
Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry
out SCOP domain assignments to all genomes at the superfamily level.
Alignments of sequences to 2 models
in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical
are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.
Browse and view proteins in genomes which have
different domain combinations including a Small protein B (SmpB) domain.
Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.
Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.
There are 2 hidden Markov models representing the Small protein B (SmpB) superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.
Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · UniProtKB KeyWords (KW) · Internal database links ]