{PDOC50126} {PS50126; S1} {PS50832; S1_IF1_TYPE} {BEGIN} ********************** * 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 ). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta 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 eIF2alpha. - 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. -Sequences known to belong to this class detected by the S1 profile: ALL except 1. -Other sequence(s) detected in Swiss-Prot: NONE. -Sequences known to belong to this class detected by the S1 IF-1 profile: ALL. -Other sequence(s) detected in Swiss-Prot: NONE. -Last update: December 2001 / First entry. [ 1] Boni I.V., Isaeva D.M., Musychenko M.L., Tzareva N.V. "Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1." Nucleic Acids Res. 19:155-162(1991). PubMed=2011495 [ 2] Ringquist S., Jones T., Snyder E.E., Gibson T., Boni I., Gold L. "High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites." Biochemistry 34:3640-3648(1995). PubMed=7534475 [ 3] Bycroft M., Hubbard T.J., Proctor M., Freund S.M., Murzin A.G. "The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold." Cell 88:235-242(1997). PubMed=9008164 [ 4] Murzin A.G. "OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences." EMBO J. 12:861-867(1993). PubMed=8458342 -------------------------------------------------------------------------------- PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html -------------------------------------------------------------------------------- {END}