Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 16.71 kDa 
• Atom Count: 1534 
• Modelled Residue Count: 151 
• Deposited Residue Count: 154 
• Unique protein chains: 1

4C6A

High Resolution Structure of the Nucleoside diphosphate kinase

• PDB DOI: 10.2210/pdb4C6A/pdb

• Classification: TRANSFERASE
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-09-18 Released: 2013-11-20 
• Deposition Author(s): Priet, S., Ferron, F., Alvarez, K., Verron, M., Canard, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.172 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Enzymatic Synthesis of Acyclic Nucleoside Thiophosphonate Diphosphates: Effect of the Alpha-Phosphorus Configuration on HIV-1 RT Activity.

Priet, S., Roux, L., Saez-Ayala, M., Ferron, F., Canard, B., Alvarez, K.

(2015) Antiviral Res 117: 122

• PubMed: 25766862 
• DOI: 10.1016/j.antiviral.2015.03.003
• Primary Citation of Related Structures:  
  4C6A, 4CP5


• PubMed Abstract: 
  

The acyclic nucleosides thiophosphonates (9-[2-(thiophosphonomethoxy)ethyl]adenine (S-PMEA) and (R)-9-[2-(thiophosphonomethoxy)propyl]adenine (S-PMPA), exhibit antiviral activity against HIV-1, -2 and HBV. Their diphosphate forms S-PMEApp and S-PMPApp, synthesized as stereoisomeric mixture, are potent inhibitors of wild-type (WT) HIV-1 RT. Understanding HIV-1 RT stereoselectivity, however, awaits resolution of the diphosphate forms into defined stereoisomers. To this aim, thiophosphonate monophosphates S-PMEAp and S-PMPAp were synthesized and used in a stereocontrolled enzyme-catalyzed phosphoryl transfer reaction involving either nucleoside diphosphate kinase (NDPK) or creatine kinase (CK) to obtain thiophosphonate diphosphates as separated isomers. We then quantified substrate preference of recombinant WT HIV-1 RT toward pure stereoisomers using in vitro steady-state kinetic analyses. The crystal structure of a complex between Dictyostelium NDPK and S-PMPApp at 2.32Å allowed to determine the absolute configuration at the α-phosphorus atom in relation to the stereo-preference of studied enzymes. The RP isomer of S-PMPApp and S-PMEApp are the preferred substrate over SP for both NDPK and HIV-1 RT.

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Organizational Affiliation: 

Laboratoire d'Architecture et Fonction des Macromolécules Biologiques, UMR CNRS 7257, Team "Antiviral Medicinal Chemistry", Université Aix-Marseille, Parc scientifique de Luminy, 163 av. de Luminy, 13288 Marseille Cedex 9, France. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC	A	154	Dictyostelium discoideum	Mutation(s): 1  Gene Names: ndkC-1, gip17, ndkB, DDB_G0273069, ndkC-2, DDB_G0273805 EC: 2.7.4.6
UniProt
Find proteins for P22887 (Dictyostelium discoideum) Explore P22887  Go to UniProtKB:  P22887

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.172 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.7	α = 90
b = 71.7	β = 90
c = 106.78	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-18 
• Released Date: 2013-11-20 
Deposition Author(s): Priet, S., Ferron, F., Alvarez, K., Verron, M., Canard, B.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2015-03-25
  Changes: Database references
• Version 1.2: 2015-04-22
  Changes: Database references