PDBsum entry 1uoc

Hydrolase

PDB id: 1uoc

Contents

Protein chains

263 a.a. *

Metals

_XE ×2

_CA ×2

Waters ×45

* Residue conservation analysis

PDB id:

1uoc

Name:

Hydrolase

Title:

X-ray structure of the rnase domain of the yeast pop2 protein

Structure:

Pop2. Chain: a, b. Fragment: rnase d domain, residues 147-433. Synonym: ccr4-associated factor 1. Engineered: yes. Other_details: 2 residues added in n-terminal because of a tev cleavable tag.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.30Å R-factor: 0.239 R-free: 0.265

Authors:

S.Thore,F.Mauxion,B.Seraphin,D.Suck

Key ref:

S.Thore et al. (2003). X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep, 4, 1150-1155. PubMed id: 14618157 DOI: 10.1038/sj.embor.7400020

Date:

16-Sep-03 Release date: 20-Nov-03

Protein chains

P39008  (POP2_YEAST) -  Poly(A) ribonuclease POP2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 433 a.a.

Struc: 263 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.13.4 - poly(A)-specific ribonuclease.
• Reaction: Exonucleolytic cleavage of poly(A) to 5'-AMP.

DOI no: 10.1038/sj.embor.7400020

EMBO Rep 4:1150-1155 (2003)

PubMed id: 14618157

X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex.

S.Thore, F.Mauxion, B.Séraphin, D.Suck.

ABSTRACT

In Saccharomyces cerevisiae, a large complex, known as the Ccr4-Not complex, containing two nucleases, is responsible for mRNA deadenylation. One of these nucleases is called Pop2 and has been identified by similarity with PARN, a human poly(A) nuclease. Here, we present the crystal structure of the nuclease domain of Pop2 at 2.3 A resolution. The domain has the fold of the DnaQ family and represents the first structure of an RNase from the DEDD superfamily. Despite the presence of two non-canonical residues in the active site, the domain displays RNase activity on a broad range of RNA substrates. Site-directed mutagenesis of active-site residues demonstrates the intrinsic ability of the Pop2 RNase D domain to digest RNA. This first structure of a nuclease involved in the 3'-5' deadenylation of mRNA in yeast provides information for the understanding of the mechanism by which the Ccr4-Not complex achieves its functions.

Selected figure(s)

Figure 1.
Figure 1 Structure of the nuclease domain of the Pop2 protein. (A) Ribbon plot representation with the secondary elements in the following colour code: -helix, red; -strands, green; and loops, yellow. (B) Crossed-eye stereo representation of the C trace is displayed with every 20th residue marked.

Figure 2.
Figure 2 Structural homology of Pop2 with members of the DEDD nuclease superfamily. (A) Structure-based sequence alignment of Pop2, the exonuclease domain of PolI and the epsilon -subunit of PolIII. Sequence conservation is shown by colour coding: invariant residues are highlighted in red. Yellow highlights residues that have similar properties. Secondary structure elements of Pop2 are shown above the sequences. Small arrowheads indicate the conserved DEDD residues forming the catalytic site of the epsilon -subunit. (B) The three structures shown in the same relative orientation. (C) The electrostatic surface potentials of Pop2 and the epsilon -subunit indicate the location of the active site; catalytic residues are highlighted. (D) Close-up view of the active site of the epsilon -subunit (salmon colour; with bound TMP in yellow) superimposed with the Pop2 (light green) structure and (E) side view of the secondary structure elements interacting with the bound nucleotide. Bold and italic labels correspond to the amino acids from Pop2 or the epsilon -subunit, respectively.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO Rep (2003, 4, 1150-1155) copyright 2003.

Figures were selected by an automated process.