6EHI

NucT from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the substrate selectivity of Helicobacter pylori NucT nuclease activity.

Celma, L.Corbinais, C.Vercruyssen, J.Veaute, X.de la Sierra-Gallay, I.L.Guerois, R.Busso, D.Mathieu, A.Marsin, S.Quevillon-Cheruel, S.Radicella, J.P.

(2017) PLoS ONE 12: e0189049

  • DOI: 10.1371/journal.pone.0189049

  • PubMed Abstract: 
  • The Phospholipase D (PLD) superfamily of proteins includes a group of enzymes with nuclease activity on various nucleic acid substrates. Here, with the aim of better understanding the substrate specificity determinants in this subfamily, we have char ...

    The Phospholipase D (PLD) superfamily of proteins includes a group of enzymes with nuclease activity on various nucleic acid substrates. Here, with the aim of better understanding the substrate specificity determinants in this subfamily, we have characterised the enzymatic activity and the crystal structure of NucT, a nuclease implicated in Helicobacter pylori purine salvage and natural transformation and compared them to those of its bacterial and mammalian homologues. NucT exhibits an endonuclease activity with a strong preference for single stranded nucleic acids substrates. We identified histidine124 as essential for the catalytic activity of the protein. Comparison of the NucT crystal structure at 1.58 Ã… resolution reported here with those of other members of the sub-family suggests that the specificity of NucT for single-stranded nucleic acids is provided by the width of a positively charged groove giving access to the catalytic site.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclease NucT
A, B, C, D, E, F, G, H, I, J, K, L
162Helicobacter pyloriMutation(s): 1 
Find proteins for A0A1V3AA65 (Helicobacter pylori)
Go to UniProtKB:  A0A1V3AA65
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, C, E, F, I, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.350α = 81.36
b = 71.370β = 74.30
c = 110.470γ = 82.33
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CEAFrance--
French Infrastructure for Integrated Structural BiologyFranceANR-10-INSB-05-01
Indo-French Centre for Promotion of Advanced researchFrance5203-5
Bourse regionale de la MartiniqueFrance--
DIM-MalinfFrance--

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release