1BUX

3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.204 
  • R-Value Observed: 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

  • DOI: 10.1074/jbc.273.44.28773
  • Primary Citation of Related Structures:  
    1BUX

  • 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 oncogene by binding to its NHE sequence ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOSIDE DIPHOSPHATE KINASEA, B, C155Dictyostelium discoideumMutation(s): 0 
Gene Names: ndkC-1gip17ndkBDDB_G0273069ndkC-2DDB_G0273805
EC: 2.7.4.6
UniProt
Find proteins for P22887 (Dictyostelium discoideum)
Explore P22887 
Go to UniProtKB:  P22887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22887
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPS
Query on PPS

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE
C10 H15 N5 O13 P2 S
GACDQMDRPRGCTN-KQYNXXCUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PPS PDBBind:  1BUX Kd: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.5α = 90
b = 71.5β = 90
c = 153.9γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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