HMM Summary Page: TIGR00086

FunctionSsrA-binding protein
Gene SymbolsmpB
Trusted Cutoff119.10
Domain Trusted Cutoff119.10
Noise Cutoff82.35
Domain Noise Cutoff82.35
Isology Typeequivalog
HMM Length144
Mainrole CategoryProtein synthesis
Subrole CategoryOther
Gene Ontology TermGO:0003723: RNA binding molecular_function
GO:0006450: regulation of translational fidelity biological_process
AuthorHaft DH
Entry DateApr 20 1999 2:09PM
Last ModifiedFeb 14 2011 3:27PM
CommentThis model describes the SsrA-binding protein, also called tmRNA binding protein, small protein B, and SmpB. The small, stable RNA SsrA (also called tmRNA or 10Sa RNA) recognizes stalled ribosomes such as occur during translation from message that lacks a stop codon. It becomes charged with Ala like a tRNA, then acts as mRNA to resume translation started with the defective mRNA. The short C-terminal peptide tag added by the SsrA system marks the abortively translated protein for degradation. SmpB binds SsrA after its aminoacylation but before the coupling of the Ala to the nascent polypeptide chain and is an essential part of the SsrA peptide tagging system. SmpB has been associated with the survival of bacterial pathogens in conditions of stress. It is universal in the first 100 sequenced bacterial genomes.
ReferencesSE TIGR AL msa RM 99321766 RT SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). RA Karzai AW, Susskind MM, Sauer RT RL EMBO J 1999 Jul 1;18(13):3793-9 DR HAMAP; MF_00023; 537 of 544
Genome PropertyGenProp0211: tmRNA trans-translation system (HMM)
GenProp0799: bacterial core gene set, exactly 1 per genome (HMM)