4UOH

Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.007 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


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Literature

Structure of Nucleoside Diphosphate Kinase from Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates

Lopez-Zavala, A.A.Quintero-Reyes, I.E.Carrasco-Miranda, J.S.Stojanoff, V.Weichsel, A.Rudino-Pinera, E.Sotelo-Mundo, R.R.

(2014) Acta Crystallogr.,Sect.F 79: 1150

  • DOI: 10.1107/S2053230X1401557X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleoside diphosphate kinase (NDK; EC 2.7.4.6) is an enzyme that catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Expression of the NDK from Litopenaeus vannamei (LvNDK) is know ...

    Nucleoside diphosphate kinase (NDK; EC 2.7.4.6) is an enzyme that catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Expression of the NDK from Litopenaeus vannamei (LvNDK) is known to be regulated under viral infection. Also, as determined by isothermal titration calorimetry, LvNDK binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with no heat of binding interaction for dCDP [Quintero-Reyes et al. (2012), J. Bioenerg. Biomembr. 44, 325-331]. In order to investigate the differences in selectivity, LvNDK was crystallized as binary complexes with both acceptor (dADP and dCDP) and donor (ADP) phosphate-group nucleoside diphosphate substrates and their structures were determined. The three structures with purine or pyrimidine nucleotide ligands are all hexameric. Also, the binding of deoxy or ribonucleotides is similar, as in the former a water molecule replaces the hydrogen bond made by Lys11 to the 2'-hydroxyl group of the ribose moiety. This allows Lys11 to maintain a catalytically favourable conformation independently of the kind of sugar found in the nucleotide. Because of this, shrimp NDK may phosphorylate nucleotide analogues to inhibit the viral infections that attack this organism.


    Organizational Affiliation

    Universidad de Sonora, Blvd Bordo Nuevo s/n, Ejido Providencia, 85039 Cd Obregón, Sonora, Mexico.,Macromolecular Crystallography Core, The University of Arizona, Biological Sciences West, 1041 East Lowell Street, Tucson, AZ 85721, USA.,National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA.,Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, 62210 Morelos, Mexico.,Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, 83304 Sonora, Mexico.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
A, B, C
151Penaeus vannameiMutation(s): 0 
EC: 2.7.4.6
Find proteins for A5J299 (Penaeus vannamei)
Go to UniProtKB:  A5J299
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.007 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 69.806α = 90.00
b = 120.835β = 90.00
c = 103.273γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-09-17
    Type: Database references