 |
PDBsum entry 3ef5
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Structure and biological function of the RNA pyrophosphohydrolase bdrpph from bdellovibrio bacteriovorus.
|
|
|
Authors
|
|
S.A.Messing,
S.B.Gabelli,
Q.Liu,
H.Celesnik,
J.G.Belasco,
S.A.Piñeiro,
L.M.Amzel.
|
|
|
Ref.
|
|
Structure, 2009,
17,
472-481.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Until recently, the mechanism of mRNA decay in bacteria was thought to be
different from that of eukaryotes. This paradigm changed with the discovery that
RppH (ORF176/NudH/YgdP), an Escherichia coli enzyme that belongs to the Nudix
superfamily, is an RNA pyrophosphohydrolase that initiates mRNA decay by
cleaving pyrophosphate from the 5'-triphosphate. Here we report the 1.9 A
resolution structure of the Nudix hydrolase BdRppH from Bdellovibrio
bacteriovorus, a bacterium that feeds on other Gram-negative bacteria. Based on
the structure of the enzyme alone and in complex with GTP-Mg(2+), we propose a
mode of RNA binding similar to that of the nuclear decapping enzyme from Xenopus
laevis, X29. In additional experiments, we show that BdRppH can indeed function
in vitro and in vivo as an RNA pyrophosphohydrolase. These findings set the
basis for the identification of possible decapping enzymes in other bacteria.
|
|
|
|
|
|
|
|
Figure 1.
Figure 1. Structure of BdRppH
(A) A “side”
representation of BdRppH with β strands shown in cyan, α
helices in magenta, and loops in brown.
(B) Vertically
rotated view (90°) of BdRppH from “above” looking down
into the active site.
|
|
Figure 4.
Figure 4. BdRppH-GTP Binding
(A) A view from “above”
looking down onto the two active sites of BdRppH, with GTP
substrate colored in yellow, magnesium ions in green, and the
surface of the protein colored according to its electrostatic
potential.
(B) Ribbon diagram of the active site of BdRppH
showing GTP and key coordinating residues; residues are depicted
in yellow, magnesium ions in magenta, and GTP in green.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Cell Press:
Structure
(2009,
17,
472-481)
copyright 2009.
|
|
|
|
|
|
|
