PROSITE documentation PDOC52002
Sm domain profile


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 β-sheet and an α-helix at the N-terminus (see <PDB:1HK9>) [1,2,5].

The profile we developed covers the entire Sm domain.

Last update:

June 2022 / First entry.


Technical section

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

SM, PS52002; Sm domain profile  (MATRIX)


1AuthorsMura C. Randolph P.S. Patterson J. Cozen A.E.
TitleArchaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function.
SourceRNA. Biol. 10:636-651(2013).
PubMed ID23579284

2AuthorsLekontseva N.V. Stolboushkina E.A. Nikulin A.D.
TitleDiversity of LSM Family Proteins: Similarities and Differences.
SourceBiochemistry. (Mosc). 86:S38-S49(2021).
PubMed ID33827399

3AuthorsPaya G. Bautista V. Camacho M. Bonete M.-J. Esclapez J.
TitleFunctional analysis of Lsm protein under multiple stress conditions in the extreme haloarchaeon Haloferax mediterranei.
SourceBiochimie 187:33-47(2021).
PubMed ID33992715

4AuthorsAchsel T. Stark H. Luhrmann R.
TitleThe Sm domain is an ancient RNA-binding motif with oligo(U) specificity.
SourceProc. Natl. Acad. Sci. U. S. A. 98:3685-3689(2001).
PubMed ID11259661

5AuthorsSauter C. Basquin J. Suck D.
TitleSm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli.
SourceNucleic. Acids. Res. 31:4091-4098(2003).
PubMed ID12853626

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