PDBsum entry 3ef5

Hydrolase

PDB id: 3ef5

Contents

Protein chains

132 a.a. *

Ligands

DGT ×2

Waters ×44

* Residue conservation analysis

PDB id:

3ef5

Name:

Hydrolase

Title:

Structure of the RNA pyrophosphohydrolase bdrpph in complex with dgtp

Structure:

Probable pyrophosphohydrolase. Chain: a, b. Engineered: yes

Source:

Bdellovibrio bacteriovorus. Organism_taxid: 959. Strain: hd100. Gene: mutt, bd0714. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.243 R-free: 0.297

Authors:

S.A.Messing,S.B.Gabelli,L.M.Amzel

Key ref:

S.A.Messing et al. (2009). Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus. Structure, 17, 472-481. PubMed id: 19278661 DOI: 10.1016/j.str.2008.12.022

Date:

08-Sep-08 Release date: 24-Mar-09

Protein chains

Q6MPX4  (Q6MPX4_BDEBA) -  8-oxo-dGTP diphosphatase from Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)

Seq: 153 a.a.

Struc: 132 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.55 - 8-oxo-dGTP diphosphatase.
• Reaction: 8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate + H⁺
• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/j.str.2008.12.022

Structure 17:472-481 (2009)

PubMed id: 19278661

Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.

S.A.Messing, S.B.Gabelli, Q.Liu, H.Celesnik, J.G.Belasco, S.A.Piñeiro, L.M.Amzel.

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.

Selected figure(s)

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.

Figures were selected by an automated process.