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.