{PDOC52002}
{PS52002; SM}
{BEGIN}
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* Sm domain profile *
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Sm, like-Sm  (Lsm),  and  Hfq  proteins  belong  to a large family of proteins
involved in  numerous  processes  associated  with  RNA  processing  and  gene
expression regulation. The members of this protein family have been identified
in all  three  domains of life: bacteria, archaea, and eukarya. The Sm and Lsm
proteins are  found in Archaea and Eukarya domains, whereas Hfq proteins exist
in the   Bacteria   domain   and   one  archaeon  species,  Methanocaldococcus
jannaschii. Heteroheptameric eukaryotic Sm and Lsm proteins participate in the
formation of  spliceosomes  and  mRNA  decapping.  Homohexameric bacterial Lsm
protein, Hfq,  is  involved  in  the  regulation of transcription of different
mRNAs by  facilitating  their  interactions  with  small  regulatory RNAs. Lsm
archaeal proteins  (SmAPs) form homoheptamers and interact with polynucleotide
phosphorylase P and uridine-rich RNA sequences, and, probably, are involved in
the processing  of  tRNAs. All these proteins contain the Sm domain consisting
of two  conserved  motifs,  Sm1  and  Sm2,  separated by a linker with varying
length and  amino acid sequence. The Sm domain is responsible for both protein
oligomerization and specific RNA binding [1,2,3,4,5].

The Sm  core  is  ~60-70  residues  in length and its fold consists of a five-
stranded beta-sheet  and  an  alpha-helix  at  the N-terminus (see <PDB:1HK9>)
[1,2,5].

The profile we developed covers the entire Sm domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: June 2022 / First entry.

[ 1] Mura C., Randolph P.S., Patterson J., Cozen A.E.
     "Archaeal and eukaryotic homologs of Hfq: A structural and
     evolutionary perspective on Sm function."
     RNA. Biol. 10:636-651(2013).
     PubMed=23579284; DOI=10.4161/rna.24538
[ 2] Lekontseva N.V., Stolboushkina E.A., Nikulin A.D.
     "Diversity of LSM Family Proteins: Similarities and Differences."
     Biochemistry. (Mosc). 86:S38-S49(2021).
     PubMed=33827399; DOI=10.1134/S0006297921140042
[ 3] Paya G., Bautista V., Camacho M., Bonete M.-J., Esclapez J.
     "Functional analysis of Lsm protein under multiple stress conditions
     in the extreme haloarchaeon Haloferax mediterranei."
     Biochimie 187:33-47(2021).
     PubMed=33992715; DOI=10.1016/j.biochi.2021.05.002
[ 4] Achsel T., Stark H., Luhrmann R.
     "The Sm domain is an ancient RNA-binding motif with oligo(U)
     specificity."
     Proc. Natl. Acad. Sci. U. S. A. 98:3685-3689(2001).
     PubMed=11259661; DOI=10.1073/pnas.071033998
[ 5] Sauter C., Basquin J., Suck D.
     "Sm-like proteins in Eubacteria: the crystal structure of the Hfq
     protein from Escherichia coli."
     Nucleic. Acids. Res. 31:4091-4098(2003).
     PubMed=12853626; DOI=10.1093/nar/gkg480

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