PDBsum entry: 1ljo

Unknown function

PDB id: 1ljo

Contents

Protein chain

75 a.a. *

Ligands

ACY ×3

Metals

_CD

Waters ×33

* Residue conservation analysis

PDB id:

1ljo

Name:

Unknown function

Title:

Crystal structure of an sm-like protein (af-sm2) from archae fulgidus at 1.95a resolution

Structure:

Archaeal sm-like protein af-sm2. Chain: a. Engineered: yes. Mutation: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: af0362. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.95Å R-factor: 0.194 R-free: 0.211

Authors:

I.Toro,J.Basquin,H.Teo-Dreher,D.Suck

Key ref:

I.Törö et al. (2002). 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. PubMed id: 12079339 DOI: 10.1016/S0022-2836(02)00406-0

Date:

22-Apr-02 Release date: 03-Jul-02

Protein chain

O29885  (O29885_ARCFU) -  SnRNP, putative

Seq: 75 a.a.

Struc: 75 a.a.

DOI no: 10.1016/S0022-2836(02)00406-0

J Mol Biol 320:129-142 (2002)

PubMed id: 12079339

Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus.

I.Törö, J.Basquin, H.Teo-Dreher, D.Suck.

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.

Selected figure(s)

Figure 5.
Figure 5. Structure of the AF-Sm1 heptamer and the AF-Sm2 hexamer. (a) Ribbon representation of the AF-Sm1 heptamer and the AF-Sm2 hexamer (top and side view). For clarity, the monomers are drawn alternately in red and green, and one monomer in AF-Sm1 is depicted in yellow. (b) Electrostatic surface charge potential showing the two faces of the rings. Shown on the left is the side binding the RNA and containing the N-terminal helix (corresponding to the top view shown in (a)). It is relatively flat, while the other side exhibits pronounced grooves emanating from the centre. These grooves are positively charged in AF-Sm1 (as indicated by the blue colour), but negatively charged in AF-Sm2, giving rise to oppositely charged faces on the rough side of the rings. The Figure was produced with GRASP.[41.]

Figure 6.
Figure 6. Dimer contacts in the AF-Sm1 (top) and AF-Sm2 (bottom) oligomers. (a) The molecules are shown as grey coloured ribbons for the pair of interacting molecules highlighting the interacting side-chains by red and blue colours. Side-chains involved in contacts (<4.0 Å), located mainly on b-strands 4 and 5 as well as the N-terminal helix, are represented in ball-and-stick mode. (b) Ionic interactions stabilising the AF-Sm1 heptamer (relevant distances (in Å) are indicated). These contacts are not present in AF-Sm2. The Figure was produced with MOLSCRIPT.[40.]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 129-142) copyright 2002.

Figures were selected by an automated process.