3B1Q

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with inosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity

Yasutake, Y.Ota, H.Hino, E.Sakasegawa, S.Tamura, T.

(2011) Acta Crystallogr D Biol Crystallogr 67: 945-956

  • DOI: 10.1107/S0907444911038777
  • Primary Citation of Related Structures:  
    3B1R, 3B1N, 3B1O, 3B1P, 3B1Q

  • PubMed Abstract: 
  • The nucleoside kinase (NK) from the mesophilic Gram-negative bacterium Burkholderia thailandensis (BthNK) is a member of the phosphofructokinase B (Pfk-B) family and catalyzes the Mg(2+)- and ATP-dependent phosphorylation of a broad range of nucleosides such as inosine (INO), adenosine (ADO) and mizoribine (MZR) ...

    The nucleoside kinase (NK) from the mesophilic Gram-negative bacterium Burkholderia thailandensis (BthNK) is a member of the phosphofructokinase B (Pfk-B) family and catalyzes the Mg(2+)- and ATP-dependent phosphorylation of a broad range of nucleosides such as inosine (INO), adenosine (ADO) and mizoribine (MZR). BthNK is currently used in clinical practice to measure serum MZR levels. Here, crystal structures of BthNK in a ligand-free form and in complexes with INO, INO-ADP, MZR-ADP and AMP-Mg(2+)-AMP are described. The typical homodimeric architecture of Pfk-B enzymes was detected in three distinct conformational states: an asymmetric dimer with one subunit in an open conformation and the other in a closed conformation (the ligand-free form), a closed conformation (the binary complex with INO) and a fully closed conformation (the other ternary and quaternary complexes). The previously unreported fully closed structures suggest the possibility that Mg(2+) might directly interact with the β- and γ-phosphates of ATP to maintain neutralization of the negative charge throughout the reaction. The nucleoside-complex structures also showed that the base moiety of the bound nucleoside is partly exposed to the solvent, thereby enabling the recognition of a wide range of nucleoside bases. Gly170 is responsible for the solvent accessibility of the base moiety and is assumed to be a key residue for the broad nucleoside recognition of BthNK. Remarkably, the G170Q mutation increases the specificity of BthNK for ADO. These findings provide insight into the conformational dynamics, catalytic mechanism and nucleoside selectivity of BthNK and related enzymes.


    Organizational Affiliation

    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Sapporo 062-8517, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribokinase, putativeABCDEF326Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: BTH_I1158
EC: 2.7.1.143
Find proteins for Q2SZE4 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264))
Explore Q2SZE4 
Go to UniProtKB:  Q2SZE4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download CCD File 
A, B, C, E
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
NOS
Query on NOS

Download CCD File 
A, B, C, D, E, F
INOSINE
C10 H12 N4 O5
UGQMRVRMYYASKQ-KQYNXXCUSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B, C, D, E, F
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B, C, D, E, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.11α = 66.33
b = 85.897β = 68.47
c = 86.872γ = 67.81
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references