1MN7 | pdb_00001mn7

NDP kinase mutant (H122G;N119S;F64W) in complex with aBAZTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.295 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.222 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Improving nucleoside diphosphate kinase for antiviral nucleotide analogs activation

gallois-montbrun, s.schneider, b.chen, y.giacomoni-fernandes, v.mulard, l.morera, s.janin, j.deville-bonne, d.veron, m.

(2002) J Biological Chem 277: 39953-39959

  • DOI: https://doi.org/10.1074/jbc.M206360200
  • Primary Citation Related Structures: 
    1MN7

  • PubMed Abstract: 

    Antiviral nucleoside analog therapies rely on their incorporation by viral DNA polymerases/reverse transcriptase leading to chain termination. The analogs (3'-deoxy-3'-azidothymidine (AZT), 2',3'-didehydro-2',3'-dideoxythymidine (d4T), and other dideoxynucleosides) are sequentially converted into triphosphate by cellular kinases of the nucleoside salvage pathway and are often poor substrates of these enzymes. Nucleoside diphosphate (NDP) kinase phosphorylates the diphosphate derivatives of the analogs with an efficiency some 10(4) lower than for its natural substrates. Kinetic and structural studies of Dictyostelium and human NDP kinases show that the sugar 3'-OH, absent from all antiviral analogs, is required for catalysis. To improve the catalytic efficiency of NDP kinase on the analogs, we engineered several mutants with a protein OH group replacing the sugar 3'-OH. The substitution of Asn-115 in Ser and Leu-55 in His results in an NDP kinase mutant with an enhanced ability to phosphorylate antiviral derivatives. Transfection of the mutant enzyme in Escherichia coli results in an increased sensitivity to AZT. An x-ray structure at 2.15-A resolution of the Dictyostelium enzyme bearing the serine substitution in complex with the R(p)-alpha-borano-triphosphate derivative of AZT shows that the enhanced activity reflects an improved geometry of binding and a favorable interaction of the 3'-azido group with the engineered serine.


  • Organizational Affiliation
    • Régulation Enzymatique des Activités Cellulaires, CNRS FRE 2364, Institut Pasteur, 25, rue du Dr. Roux 75724, Paris cedex 15, France.

Macromolecule Content 

  • Total Structure Weight: 34.55 kDa 
  • Atom Count: 2,653 
  • Modeled Residue Count: 300 
  • Deposited Residue Count: 310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NDP kinase
A, B
155Dictyostelium discoideumMutation(s): 3 
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.295 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.222 (DCC) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.238α = 90
b = 71.238β = 90
c = 106.677γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-02
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-29
    Changes: Data collection