3VAQ

Adenosine kinase from Schistosoma mansoni in complex with adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Adenosine kinase from Schistosoma mansoni: structural basis for the differential incorporation of nucleoside analogues.

Romanello, L.Bachega, J.F.Cassago, A.Brandao-Neto, J.Demarco, R.Garratt, R.C.Pereira, H.D.

(2013) Acta Crystallogr.,Sect.D 69: 126-136

  • DOI: 10.1107/S0907444912044800
  • Primary Citation of Related Structures:  3UQ6, 3UQ9, 3VAS, 4DC3

  • PubMed Abstract: 
  • In adult schistosomes, the enzyme adenosine kinase (AK) is responsible for the incorporation of some adenosine analogues, such as 2-fluoroadenosine and tubercidin, into the nucleotide pool, but not others. In the present study, the structures of four ...

    In adult schistosomes, the enzyme adenosine kinase (AK) is responsible for the incorporation of some adenosine analogues, such as 2-fluoroadenosine and tubercidin, into the nucleotide pool, but not others. In the present study, the structures of four complexes of Schistosoma mansoni AK bound to adenosine and adenosine analogues are reported which shed light on this observation. Two differences in the adenosine-binding site in comparison with the human counterpart (I38Q and T36A) are responsible for their differential specificities towards adenosine analogues, in which the Schistosoma enzyme does not tolerate bulky substituents at the N7 base position. This aids in explaining experimental data which were reported in the literature more than two decades ago. Furthermore, there appears to be considerable plasticity within the substrate-binding sites that affects the side-chain conformation of Ile38 and causes a previously unobserved flexibility within the loop comprising residues 286-299. These results reveal that the latter can be sterically occluded in the absence of ATP. Overall, these results contribute to the body of knowledge concerning the enzymes of the purine salvage pathway in this important human parasite.


    Organizational Affiliation

    Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative adenosine kinase
A, B
372Schistosoma mansoniEC: 2.7.1.20
Find proteins for G4V7G8 (Schistosoma mansoni)
Go to UniProtKB:  G4V7G8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
A, B
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.100α = 90.00
b = 180.310β = 90.00
c = 79.430γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
DNAdata collection
XDSdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2013-01-16
    Type: Database references