1LJO

CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION

Summary for 1LJO

• Entry DOI: 10.2210/pdb1ljo/pdb
• Related: 1B34 1D3B 1I4K 1I5L 1I81 1I8F 1JRI
• Descriptor: Archaeal Sm-like protein AF-Sm2, CADMIUM ION, ACETIC ACID, ... (4 entities in total)
• Functional Keywords: snrnp, sm, core snrnp domain, rna binding protein, unknown function
• Biological source: Archaeoglobus fulgidus
• Total number of polymer chains: 1
• Total formula weight: 8909.61

Authors

Toro, I.,Basquin, J.,Teo-Dreher, H.,Suck, D. (deposition date: 2002-04-22, release date: 2002-07-03, Last modification date: 2024-04-03)

Primary citation

Toro, I.,Basquin, J.,Teo-Dreher, H.,Suck, D.
Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus.
J.Mol.Biol., 320:129-142, 2002

PubMed Abstract: 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.

PubMed: 12079339
DOI: 10.1016/S0022-2836(02)00406-0

Experimental method

X-RAY DIFFRACTION (1.95 Å)