PROSITE documentation PDOC50126
S1 domain profiles


The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity [1,2].

The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined [3]. It displays some similarity with the cold shock domain (CSD) (see <PDOC00304>). Both the S1 and the CSD domain consist of an antiparallel β barrel of the same topology with 5 β strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold [4]. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site [3].

Some of the proteins in which an S1 domain is found are listed below.

  • Eukaryotic translation initiation factor eIF2α.
  • Yeast protein PRP22. A RNA helicase required for the release of mRNA from the spliceosome.
  • Archaeal and eukaryotic DNA dependent RNA polymerase II subunit 5.
  • Eukaryotic rRNA biogenesis protein RRP5. Required for the formation of 18S and 5,8S rRNA.
  • Eukaryotic dead box protein 8. Facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome.
  • Bacterial and chloroplastic translation initiation factor 1 (IF-1).
  • Bacterial and chloroplastic S1 protein. Plays an essential role in facilitating the initiation of translation by interacting with both ribosome and with sequences in mRNA upstream from the ribosome-binding site.
  • Bacterial N-utilization substance protein A homolog (nusA). Could participates in both the termination and antitermination of transcription.
  • Bacterial Ribonuclease E. Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of Cole1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover.
  • Bacterial ribonuclease G. Involved in processing of the 5'end of 16S rRNA. Could also be involved in chromosome segregation and cell division.
  • Bacterial exoribonuclease II. Acts on single-stranded polyribonucleotides processively in the 3' to 5' direction.
  • Bacterial ribonuclease R.
  • Bacterial polynucleotide phosphorylase (PNPase). Exonuclease that degrades mRNA in a 3'-to-5' direction, contains an S1 motif at the C-terminus immediately after a KH domain.

To identify S1 domains we developed 2 profiles, one is specific for bacterial, chloroplastic and eukaryotic IF-1 proteins. The other recognize all other S1 domains. Both profiles cover the whole domain.

Last update:

December 2001 / First entry.


Technical section

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

S1, PS50126; S1 domain profile  (MATRIX)

S1_IF1_TYPE, PS50832; S1 domain IF1 type profile  (MATRIX)


1AuthorsBoni I.V. Isaeva D.M. Musychenko M.L. Tzareva N.V.
TitleRibosome-messenger recognition: mRNA target sites for ribosomal protein S1.
SourceNucleic Acids Res. 19:155-162(1991).
PubMed ID2011495

2AuthorsRingquist S. Jones T. Snyder E.E. Gibson T. Boni I. Gold L.
TitleHigh-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites.
SourceBiochemistry 34:3640-3648(1995).
PubMed ID7534475

3AuthorsBycroft M. Hubbard T.J. Proctor M. Freund S.M. Murzin A.G.
TitleThe solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
SourceCell 88:235-242(1997).
PubMed ID9008164

4AuthorsMurzin A.G.
TitleOB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences.
SourceEMBO J. 12:861-867(1993).
PubMed ID8458342

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