2Q5Z

Crystal structure of iMazG from Vibrio DAT 722: Ntag-iMazG (P43212)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A putative house-cleaning enzyme encoded within an integron array: 1.8 A crystal structure defines a new MazG subtype.

Robinson, A.Guilfoyle, A.P.Harrop, S.J.Boucher, Y.Stokes, H.W.Curmi, P.M.Mabbutt, B.C.

(2007) Mol Microbiol 66: 610-621

  • DOI: 10.1111/j.1365-2958.2007.05932.x
  • Primary Citation of Related Structures:  
    2Q73, 2Q5Z, 2Q9L

  • PubMed Abstract: 
  • Mobile gene cassettes collectively contain a highly diverse pool of novel genes that encode many novel adaptive functions. In the non-clinical context, the function of almost all of the encoded proteins remains unknown despite the enormous size of th ...

    Mobile gene cassettes collectively contain a highly diverse pool of novel genes that encode many novel adaptive functions. In the non-clinical context, the function of almost all of the encoded proteins remains unknown despite the enormous size of this mobile gene pool. We have been characterizing cassette arrays by taking advantage of the fact that they cluster at discrete sites in chromosomes; even large arrays are thus recoverable in a relatively small number of clones in genomic libraries. In one assembled array of 116 cassettes from the marine bacterium Vibrio sp. DAT722, a putative MazG protein is encoded within the 21st cassette. Because MazG proteins are implicated in a number of cellular processes, including house-cleaning and stress survival, the presence of such a protein in a mobile cassette was noteworthy. Here we solve the crystal structure of this alpha-helical protein, and define both open and closed states of a new variant of the MazG family. Functional assays confirm that the protein is a dNTP pyrophosphohydrolase, with marked preferences for dCTP and dATP. We hypothesize that iMazG acts as a house-cleaning enzyme, preventing the incorporation of damaging non-canonical nucleotides into host-cell DNA.


    Organizational Affiliation

    Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical proteinAB114Vibrio sp. DAT722Mutation(s): 1 
Gene Names: imazG
EC: 3.6.1.19
Find proteins for Q2F9Z1 (Vibrio sp. DAT722)
Explore Q2F9Z1 
Go to UniProtKB:  Q2F9Z1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.333α = 90
b = 63.333β = 90
c = 163.227γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance