PS50889

S4 RNA-binding domain profile

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Short nameS4

Description

The S4 domain is a small globular domain consisting of 60-65 amino acid residues that is found in: - The ribosomal protein S4 family. - Tyrosyl-tRNA synthetases. - The rluA and rsuA families of pseudouridine synthases. - Several predicted RNA methylases. - A putative novel RNA editing enzyme. - A number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain typically occurs in a single copy at various positions in different proteins. The S4 domain can be found alone as in several small bacterial proteins (e.g. YabO from B. subtilis and YrfH from E. coli), or in association with other domains such as the N-terminal alpha helix rich globular domain found in S4 proteins, the pseudouridine synthase catalytic domain, the methylase domain, the tyrosyl-tRNA synthetases domain or the deaminase domain. It has been proposed that the S4 domain is capable of recognizing complex, unique 3D features in highly folded RNA molecules such as rRNAs, tRNAs, and untranslated regions of mRNAs
[4]
. The S4 domain contains a characteristic pattern of conserved polar, hydrophobic, and small residues in its N-terminal and central parts. The C- terminal part does not show a high degree of conservation between different families within the superfamily of S4 containing proteins and may be important for interactions specific to each family
[4]
. The S4 domain has an alpha/beta structure consisting of an antiparallel beta sheet packed against alpha helices
[1]
[3]
[2]
. The profile we developed covers the entire S4 RNA-binding domain.

References

1.The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif. Davies C, Gerstner RB, Draper DE, Ramakrishnan V, White SW. EMBO J. 17, 4545-58, (1998). View articlePMID: 9707415

2.Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Sivaraman J, Sauve V, Larocque R, Stura EA, Schrag JD, Cygler M, Matte A. Nat. Struct. Biol. 9, 353-8, (2002). PMID: 11953756

3.Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase. Guijarro JI, Pintar A, Prochnicka-Chalufour A, Guez V, Gilquin B, Bedouelle H, Delepierre M. Structure 10, 311-7, (2002). View articlePMID: 12005430

4.Novel predicted RNA-binding domains associated with the translation machinery. Aravind L, Koonin EV. J. Mol. Evol. 48, 291-302, (1999). View articlePMID: 10093218

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