3Q89

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with CDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase.

Srivastava, S.K.Rajasree, K.Gopal, B.

(2011) Biochim.Biophys.Acta --: --

  • DOI: 10.1016/j.bbapap.2011.06.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug-an application that has been actively pursued for a variet ...

    Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug-an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme.


    Organizational Affiliation

    Indian Institute of Science, Bangalore, India. sandeep@mbu.iisc.ernet.in




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside diphosphate kinase
A, B, C, D, E, F, G, H
157Staphylococcus aureus (strain COL)Mutation(s): 0 
Gene Names: ndk
EC: 2.7.4.6
Find proteins for Q5HFV4 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  Q5HFV4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CDP
Query on CDP

Download SDF File 
Download CCD File 
B, E
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 186.613α = 90.00
b = 73.055β = 108.23
c = 102.272γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
MAR345dtbdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-27
    Type: Initial release