3EES

Structure of the RNA pyrophosphohydrolase BdRppH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

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

(2009) Structure 17: 472-481

  • DOI: 10.1016/j.str.2008.12.022
  • Structures With Same Primary Citation

  • PubMed 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 a ...

    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 Angstroms 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-Mg2+, 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.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable pyrophosphohydrolase
A, B
153Bdellovibrio bacteriovorusMutation(s): 0 
Gene Names: mutTBd0714
EC: 3.6.1
Find proteins for Q6MPX4 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100))
Go to UniProtKB:  Q6MPX4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.491α = 90
b = 70.491β = 90
c = 100.481γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description