2YEU

Structural and functional insights of DR2231 protein, the MazG-like nucleoside triphosphate pyrophosphohydrolase from Deinococcus radiodurans, complex with Gd


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans.

Goncalves, A.M.D.Desanctis, D.Mcsweeney, S.M.

(2011) J Biol Chem 286: 30691

  • DOI: https://doi.org/10.1074/jbc.M111.247999
  • Primary Citation of Related Structures:  
    2YEU, 2YF3, 2YF4, 2YF9, 2YFC, 2YFD

  • PubMed Abstract: 

    Deinococcus radiodurans is among the very few bacterial species extremely resistant to ionizing radiation, UV light, oxidizing agents, and cycles of prolonged desiccation. The proteome of D. radiodurans reflects the evolutionary pressure exerted by chronic exposure to (nonradioactive) forms of DNA and protein damage. A clear example of this adaptation is the overrepresentation of protein families involved in the removal of non-canonical nucleoside triphosphates (NTPs) whose incorporation into nascent DNA would promote mutagenesis and DNA damage. The three-dimensional structure of the DR2231 protein has been solved at 1.80 Å resolution. This protein had been classified as an all-α-helical MazG-like protein. The present study confirms that it holds the basic structural module characteristic of the MazG superfamily; two helices form a rigid domain, and two helices form a mobile domain and connecting loops. Contrary to what is known of MazG proteins, DR2231 protein shows a functional affinity with dUTPases. Enzymatic and isothermal calorimetry assays have demonstrated high specificity toward dUTP but an inability to hydrolyze dTTP, a typical feature of dUTPases. Co-crystallization with the product of hydrolysis, dUMP, in the presence of magnesium or manganese cations, suggests similarities with the dUTP/dUDP hydrolysis mechanism reported for dimeric dUTPases. The genome of D. radiodurans encodes for all enzymes required for dTTP synthesis from dCMP, thus bypassing the need of a dUTPase. We postulate that DR2231 protein is not essential to D. radiodurans and rather performs "house-cleaning" functions within the framework of oxidative stress response. We further propose DR2231 protein as an evolutionary precursor of dimeric dUTPases.


  • Organizational Affiliation

    Macromolecular Crystallography Group, European Synchrotron Radiation Facility, Rue Jules Horowitz 6, 38043 Grenoble Cedex, France. Electronic address: seanmcs@esrf.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DR2231
A, B, C, D, E
A, B, C, D, E, F
154Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
EC: 3.6.1.19
UniProt
Find proteins for Q9RS96 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RS96 
Go to UniProtKB:  Q9RS96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RS96
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GD
Query on GD

Download Ideal Coordinates CCD File 
AA [auth C]
JA [auth D]
N [auth A]
PA [auth E]
V [auth B]
AA [auth C],
JA [auth D],
N [auth A],
PA [auth E],
V [auth B],
WA [auth F]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
G [auth A]
H [auth A]
I [auth A]
BA [auth D],
CA [auth D],
G [auth A],
H [auth A],
I [auth A],
KA [auth E],
LA [auth E],
MA [auth E],
O [auth B],
P [auth B],
QA [auth F],
RA [auth F],
SA [auth F],
W [auth C],
X [auth C],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
GA [auth D]
HA [auth D]
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
IA [auth D],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
NA [auth E],
OA [auth E],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
TA [auth F],
U [auth B],
UA [auth F],
VA [auth F],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.82α = 90
b = 110.75β = 90
c = 165.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Database references, Non-polymer description, Version format compliance