1NB2

Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase.

Chen, C.-J.Liu, M.-Y.Chang, T.Chang, W.-C.Wang, B.-C.Le Gall, J.

(2003) J.Struct.Biol. 142: 247-255


  • PubMed Abstract: 
  • We found that when grown under anaerobic conditions the moderate halophile, gram-positive bacterium Bacillus halodenitrificans (ATCC 49067) synthesizes large amounts of a polypeptide complex that contains a heme center capable of reversibly bind nitr ...

    We found that when grown under anaerobic conditions the moderate halophile, gram-positive bacterium Bacillus halodenitrificans (ATCC 49067) synthesizes large amounts of a polypeptide complex that contains a heme center capable of reversibly bind nitric oxide. This complex, when exposed to air, dissociates and reassociates into two active components, a Mn-containing superoxide dismutase (SOD) and a nucleoside diphosphate kinase (BhNDK). The crystal structure of this latter enzyme has been determined at 2.2A resolution using molecular replacement method, based on the crystal structure of Drosophila melanogaster NDK. The model contains 149 residues of a total 150 residues and 34 water molecules. BhNDK consists of a four-stranded antiparallel beta-sheet, whose surfaces are partially covered by six alpha-helices, and its overall and active site structures are similar to those of homologous enzymes. However, the hexameric packing of BhNDK shows that this enzyme is different from both eukaryotic and gram-negative bacteria. The need for the bacterium to presynthesize both SOD and NDK precursors which are activated during the anaerobic-aerobic transition is discussed.


    Organizational Affiliation

    X-ray Structural Biology Group, National Synchrotron Radiation Research Center, Hsinchu 30077, Taiwan. cjchen@srrc.gov.tw




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside Diphosphate Kinase
A
150Virgibacillus halodenitrificansMutation(s): 0 
Gene Names: ndk
EC: 2.7.4.6
Find proteins for Q7SIA9 (Virgibacillus halodenitrificans)
Go to UniProtKB:  Q7SIA9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • Space Group: P 43 3 2
Unit Cell:
Length (Å)Angle (°)
a = 114.070α = 90.00
b = 114.070β = 90.00
c = 114.070γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance