1HHQ

Role of active site resiude Lys16 in Nucleoside Diphosphate Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of Phosphoryl Transfer by Nucleoside Diphosphate Kinase Ph-Dependence and Role of Active Site Lys16 and Tyr56 Residues

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

(2001) Eur J Biochem 268: 1964

  • DOI: 10.1046/j.1432-1327.2001.02070.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nucleoside diphosphate (NDP) kinase phosphorylates nucleoside diphosphates with little specificity for the base and the sugar. Although nucleotide analogues used in antiviral therapies are also metabolized to their triphosphate form by NDP kinase, th ...

    Nucleoside diphosphate (NDP) kinase phosphorylates nucleoside diphosphates with little specificity for the base and the sugar. Although nucleotide analogues used in antiviral therapies are also metabolized to their triphosphate form by NDP kinase, their lack of the 3'-hydroxyl of the ribose, which allows them to be DNA chain terminators, severely impairs the catalytic efficiency of NDP kinase. We have analyzed the kinetics parameters of several mutant NDP kinases modified on residues (Lys16, Tyr56, Asn119) interacting with the gamma-phosphate and/or the 3'-OH of the Mg2+-ATP substrate. We compared the relative contributions of the active-site residues and the substrate 3'-OH for point mutations on Lys16, Tyr56 and Asn119. Analysis of additional data from pH profiles identify the ionization state of these residues in the enzyme active form. X-ray structure of K16A mutant NDP kinase shows no detectable rearrangement of the residues of the active site.


    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
155Dictyostelium discoideumMutation(s): 1 
Gene Names: ndkC-1gip17ndkBDDB_G0273069ndkC-2DDB_G0273805
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
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.15α = 90
b = 72.15β = 90
c = 107γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other