Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus.
Proteins of largely unknown function related to the Sm proteins present in the core domain of eukaryotic small nuclear ribonucleoprotein particles have recently been detected in Archaea. In contrast to eukaryotes, Archaea contain maximally two distinct Sm-related proteins belonging to different subfamilies, we refer to as Sm1 and Sm2. Here we report the crystal structures of the Sm1- and Sm2-type proteins from the hyperthermophilic euryarchaeon Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) at a resolution of 2.5 and 1.95 A, respectively. While the AF-Sm1 protein forms a heptameric ring structure similar to that found in other archaeal Sm1-type proteins, the AF-Sm2 protein unexpectedly forms a homo-hexamer in the crystals, and, as is evident from the mass spectrometric analysis, also in solution. Both proteins have essentially the same monomer fold and inter-subunit beta-sheet hydrogen bonding giving rise to a similar overall architecture of the doughnut-shaped six and seven-membered rings. In addition, a conserved uracil-binding pocket identified previously in an AF-Sm1/RNA complex, suggests a common RNA-binding mode for the AF-Sm1 and AF-Sm2 proteins, in line with solution studies showing preferential binding to U-rich oligonucleotides for both proteins. Clear differences are however seen in the charge distribution within the two structures. The rough faces of the rings, i.e. the faces not containing the base binding pockets, have opposite charges in the two structures, being predominantly positive in AF-Sm1 and negative in AF-Sm2. Differences in the ionic interactions between subunits provide an explanation for the distinctly different oligomerisation behaviour of the AF-Sm1 and AF-Sm2 proteins and of Sm1- and Sm2-type proteins in general, as well as the stability of their complexes. Implications for the functions of archaeal Sm proteins are being discussed.
Törö
Imre
I
Structural and Computational Biology Programme, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
Basquin
Jérôme
J
Teo-Dreher
Hiang
H
Suck
Dietrich
D
D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019611:Archaeoglobus fulgidus / Q000737:chemistry*; D018360:Crystallography, X-Ray; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017411:Ribonucleoproteins, Small Nuclear / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
D019843:Archaeal Proteins; D046911:Macromolecular Substances; D016601:RNA-Binding Proteins; D017411:Ribonucleoproteins, Small Nuclear; C426828:Sm1 protein, Archaeoglobus fulgidus; C426829:Sm2 protein, Archaeoglobus fulgidus