PDBsum entry 2po2

Hydrolase/hydrolase

PDB id: 2po2

Contents

Protein chains

236 a.a. *

267 a.a. *

Ligands

CDP

MPD ×5

Waters ×176

* Residue conservation analysis

PDB id:

2po2

Name:

Hydrolase/hydrolase

Title:

Crystal structure of the p. Abyssi exosome rnase ph ring complexed with cdp

Structure:

Probable exosome complex exonuclease 1. Chain: a. Engineered: yes. Probable exosome complex exonuclease 2. Chain: b. Engineered: yes

Source:

Pyrococcus abyssi. Organism_taxid: 29292. Gene: rrp41. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rrp42.

Resolution:

2.41Å R-factor: 0.186 R-free: 0.259

Authors:

M.V.A.S.Navarro,B.G.Guimaraes

Key ref:

M.V.Navarro et al. (2008). Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J Biol Chem, 283, 14120-14131. PubMed id: 18353775 DOI: 10.1074/jbc.M801005200

Date:

25-Apr-07 Release date: 18-Mar-08

Protein chain

Q9V119  (RRP41_PYRAB) -  Exosome complex component Rrp41 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 249 a.a.

Struc: 236 a.a.

Protein chain

Q9V118  (RRP42_PYRAB) -  Exosome complex component Rrp42 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 274 a.a.

Struc: 267 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.1.13.- - ?????

DOI no: 10.1074/jbc.M801005200

J Biol Chem 283:14120-14131 (2008)

PubMed id: 18353775

Insights into the mechanism of progressive RNA degradation by the archaeal exosome.

M.V.Navarro, C.C.Oliveira, N.I.Zanchin, B.G.Guimarães.

ABSTRACT

Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyrococcus abyssi exosome, one of them containing three 10-mer RNA strands within the exosome catalytic chamber, and report additional nucleotide interactions involving positions N5 and N7. Residues from all three Rrp41-Rrp42 heterodimers interact with a single RNA molecule, providing evidence for the functional relevance of exosome ring-like assembly in RNA processivity. Furthermore, an ADP-bound structure showed a rearrangement of nucleotide interactions at site N1, suggesting a rationale for the elimination of nucleoside diphosphate after catalysis. In combination with RNA degradation assays performed with mutants of key amino acid residues, the structural data presented here provide support for a model of exosome-mediated RNA degradation that integrates the events involving catalytic cleavage, product elimination, and RNA translocation. Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation.

Selected figure(s)

Figure 2.
FIGURE 2. P. abyssi exosome RNA recognition cleft. Rrp41 and Rrp42 subunits are colored in blue and light brown, respectively. Heterodimers forming the hexameric ring are assigned 1 to 3 and numbers in parentheses identify residues from the same dimer. a, schematic representation of the N1 to N5 binding sites. Residues involved in RNA interaction are labeled and shown in sticks. Residues mutated in this work are indicated with a colored star. b, schematic representation showing the RNA-exosome interactions in detail. c, stereo view of the N1 nucleotide binding site. The |F[o]| - |F[c]| electron density map contoured at 4 is superposed on the solvent atoms.

Figure 7.
FIGURE 7. Schematic representation of the archaeal exosome RNA processing mechanism. Inorganic phosphate and PB moiety of the nucleoside diphosphate are represented in red. Green arrows indicate structural rearrangements putatively involved in the mechanism.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 14120-14131) copyright 2008.

Figures were selected by an automated process.