 |
PDBsum entry 1uoc
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
X-Ray structure and activity of the yeast pop2 protein: a nuclease subunit of the mRNA deadenylase complex.
|
|
|
Authors
|
|
S.Thore,
F.Mauxion,
B.Séraphin,
D.Suck.
|
|
|
Ref.
|
|
EMBO Rep, 2003,
4,
1150-1155.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
