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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 . 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 . 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 .
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
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
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
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.
December 2001 / First entry.
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