PROSITE documentation PDOC50126

S1 domain profiles

Description

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)
Sequences known to belong to this class detected by the S1 profile: ALL except 1
Other sequence(s) detected in Swiss-Prot: NONE.
• Domain architecture view of Swiss-Prot proteins matching PS50126
PS50126
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50126
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50126
• Scan Swiss-Prot/TrEMBL entries against PS50126
• view ligand binding statistics
Matching PDB structures: 1E3P 1GO3 1K0R 1KL9 ... [ALL]
S1_IF1_TYPE, PS50832; S1 domain IF1 type profile  (MATRIX)
Sequences known to belong to this class detected by the S1 IF-1 profile: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Domain architecture view of Swiss-Prot proteins matching PS50832
PS50832
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50832
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50832
• Scan Swiss-Prot/TrEMBL entries against PS50832
• view ligand binding statistics
Matching PDB structures: 1AH9 1D7Q 1HR0 1JT8 ... [ALL]

References

1 Authors Boni I.V., Isaeva D.M., Musychenko M.L., Tzareva N.V.
Title Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1.
Source Nucleic Acids Res. 19:155-162(1991).
PubMed ID 2011495
2 Authors Ringquist S., Jones T., Snyder E.E., Gibson T., Boni I., Gold L.
Title High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites.
Source Biochemistry 34:3640-3648(1995).
PubMed ID 7534475
3 Authors Bycroft M., Hubbard T.J., Proctor M., Freund S.M., Murzin A.G.
Title The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
Source Cell 88:235-242(1997).
PubMed ID 9008164
4 Authors Murzin A.G.
Title OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences.
Source EMBO J. 12:861-867(1993).
PubMed ID 8458342

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