1BUX

3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.

Schneider, B.Xu, Y.W.Janin, J.Veron, M.Deville-Bonne, D.

(1998) J.Biol.Chem. 273: 28773-28778


  • PubMed Abstract: 
  • Nucleoside diphosphate (NDP) kinase catalyzes the phosphorylation of ribo- and deoxyribonucleosides diphosphates into triphosphates. NDP kinase is also involved in malignant tumors and was shown to activate in vitro transcription of the c-myc oncogen ...

    Nucleoside diphosphate (NDP) kinase catalyzes the phosphorylation of ribo- and deoxyribonucleosides diphosphates into triphosphates. NDP kinase is also involved in malignant tumors and was shown to activate in vitro transcription of the c-myc oncogene by binding to its NHE sequence. The structure of the complex of NDP kinase with bound ADP shows that the nucleotide adopts a different conformation from that observed in other phosphokinases with an internal H bond between the 3'-OH and the beta-O made free by the phosphate transfer. We use intrinsic protein fluorescence to investigate the inhibitory and binding potential of nucleotide analogues phosphorylated in 3'-OH position of the ribose to both wild type and F64W mutant NDP kinase from Dictyostelium discoideum. Due to their 3'-phosphate, 5'-phosphoadenosine 3'-phosphate (PAP) and adenosine 3'-phosphate 5'-phosphosulfate (PAPS) can be regarded as structural analogues of enzyme-bound ADP. The KD of PAPS (10 microM) is three times lower than the KD of ADP. PAPS also acts as a competitive inhibitor toward natural substrates during catalysis, with a KI in agreement with binding data. The crystal structure of the binary complex between Dictyostelium NDP kinase and PAPS was solved at 2.8-A resolution. It shows a new mode of nucleotide binding at the active site with the 3'-phosphate of PAPS located near the catalytic histidine, at the same position as the gamma-phosphate in the transition state. The sulfate group is directed toward the protein surface. PAPS will be useful for the design of high affinity drugs targeted to NDP kinases.


    Related Citations: 
    • Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase
      Morera, S.,Lascu, I.,Dumas, C.,Lebras, G.,Briozzo, P.,Veron, M.,Janin, J.
      (1994) Biochemistry 33: 459
    • Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium
      Morera, S.,Chiadmi, M.,Lebras, G.,Lascu, I.,Janin, J.
      (1995) Biochemistry 34: 11062


    Organizational Affiliation

    Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 1773, Institut Pasteur, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
A, B, C
155Dictyostelium discoideumGene Names: ndkC-1, ndkC-2 (gip17, ndkB, gip17, ndkB)
EC: 2.7.4.6
Find proteins for P22887 (Dictyostelium discoideum)
Go to UniProtKB:  P22887
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPS
Query on PPS

Download SDF File 
Download CCD File 
A, B, C
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE
C10 H15 N5 O13 P2 S
GACDQMDRPRGCTN-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PPSKd: 14000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.500α = 90.00
b = 71.500β = 90.00
c = 153.900γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance