PDBsum entry: 2br2

Hydrolase

PDB id: 2br2

Contents

Protein chains

(+ 6 more) 260 a.a. *

(+ 6 more) 241 a.a. *

Metals

_CL ×13

Waters ×98

* Residue conservation analysis

PDB id:

2br2

Name:

Hydrolase

Title:

Rnase ph core of the archaeal exosome

Structure:

Exosome complex exonuclease 2. Chain: a, c, e, g, i, k, m, o, q, s, u, w. Synonym: exosome complex exonuclease rrp41-rrp42. Engineered: yes. Exosome complex exonuclease 1. Chain: b, d, f, h, j, l, n, p, r, t, v, x. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.80Å R-factor: 0.216 R-free: 0.237

Authors:

E.Lorentzen,S.Fribourg,E.Conti

Key ref:

E.Lorentzen et al. (2005). The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct Mol Biol, 12, 575-581. PubMed id: 15951817 DOI: 10.1038/nsmb952

Date:

30-Apr-05 Release date: 06-Jun-05

Protein chains

Q9UXC0  (ECX2_SULSO) -  Probable exosome complex exonuclease 2

Seq: 275 a.a.

Struc: 260 a.a.

Protein chains

Q9UXC2  (ECX1_SULSO) -  Probable exosome complex exonuclease 1

Seq: 248 a.a.

Struc: 241 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: exosome (RNase complex) (2 terms)
• Biological process: RNA processing (2 terms)
• Biochemical function: hydrolase activity (7 terms)

DOI no: 10.1038/nsmb952

Nat Struct Mol Biol 12:575-581 (2005)

PubMed id: 15951817

The archaeal exosome core is a hexameric ring structure with three catalytic subunits.

E.Lorentzen, P.Walter, S.Fribourg, E.Evguenieva-Hackenberg, G.Klug, E.Conti.

ABSTRACT

The exosome is a 3' --> 5' exoribonuclease complex involved in RNA processing. We report the crystal structure of the RNase PH core complex of the Sulfolobus solfataricus exosome determined at a resolution of 2.8 A. The structure reveals a hexameric ring-like arrangement of three Rrp41-Rrp42 heterodimers, where both subunits adopt the RNase PH fold common to phosphorolytic exoribonucleases. Structure-guided mutagenesis reveals that the activity of the complex resides within the active sites of the Rrp41 subunits, all three of which face the same side of the hexameric structure. The Rrp42 subunit is inactive but contributes to the structuring of the Rrp41 active site. The high sequence similarity of this archaeal exosome to eukaryotic exosomes and its high structural similarity to the bacterial mRNA-degrading PNPase support a common basis for RNA-degrading machineries in all three domains of life.

Selected figure(s)

Figure 2.
Figure 2. Structure of the RNase PH ring of the S. solfataricus exosome. The two exosomal components Rrp41 (blue) and Rrp42 (green) assemble into a hexameric ring. (a) Ribbon representations viewing the structure from two opposite directions, the front view on the left and the back view on the right. This figure and all others representing structures and surfaces were generated with PyMOL (http://pymol.sourceforge.net). (b) Molecular surface representation in the same view and colors as in a. Highlighted in orange are the catalytic sites discussed in the text (Asp182 of Rrp41).

Figure 4.
Figure 4. Conserved molecular interactions and surfaces of the exosomal core. (a) The front side of the exosome features a set of positively charged residues adjacent to the Rrp41 catalytic site. The inset is shown in the same view as the front surface representation above. (b) The back side of the exosome features a large patch of residues well conserved among S. solfataricus and eukaryotic Rrp41 proteins (S. cerevisiae, Schizosaccharomyces pombe, H. sapiens, Caenorhabditis elegans and Mus musculus). The molecular surface at the top is in the same orientation as in Figure 2b, right panel, and is colored according to sequence conservation between archaeal and eukaryotic exosomes (orange, conserved residues; white, variable residues; see alignment in Supplementary Fig. 2).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 575-581) copyright 2005.

Figures were selected by an automated process.