2ABS

Crystal structure of T. gondii adenosine kinase complexed with AMP-PCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Toxoplasma gondii adenosine kinase in complex with an ATP analog at 1.1 angstroms resolution.

Zhang, Y.El Kouni, M.H.Ealick, S.E.

(2006) Acta Crystallogr.,Sect.D 62: 140-145

  • DOI: 10.1107/S090744490503430X

  • PubMed Abstract: 
  • The obligate intracellular parasite Toxoplasma gondii is incapable of synthesizing purine nucleotides de novo and relies completely on purines salvaged from the host cells. Adenosine is the preferred precursor and is phosphorylated by adenosine kinas ...

    The obligate intracellular parasite Toxoplasma gondii is incapable of synthesizing purine nucleotides de novo and relies completely on purines salvaged from the host cells. Adenosine is the preferred precursor and is phosphorylated by adenosine kinase (AK), the most active enzyme in adenosine metabolism in T. gondii. AK thus represents a potential chemotherapeutic target for the treatment of T. gondii infections. The previously solved structures of unliganded AK and AK in complex with adenosine (or 7-iodotubercidin) and an ATP analog revealed a novel catalytic mechanism. A domain closure triggered by a GG switch upon adenosine binding sequesters the adenosine and gamma-phosphate of ATP from the solvent. The formation of the anion hole induced by the ATP binding completes the structural requirements for catalysis. In the current study, the structure of a binary complex of AK and the non-hydrolysable ATP analog AMP-PCP was determined to 1.1 angstroms resolution. The overall structure is similar to the apoenzyme, with an open conformation. AMP-PCP is bound in two relaxed conformations and without anchoring by Arg136. The induced anion hole is the same as that in the ternary complex AK-adenosine-AMP-PCP. This structure provides direct evidence that ATP binding at millimolar concentrations does not require adenosine binding as a prerequisite.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
adenosine kinase
A
383Toxoplasma gondiiMutation(s): 5 
Gene Names: AK
EC: 2.7.1.20
Find proteins for Q9TVW2 (Toxoplasma gondii)
Go to UniProtKB:  Q9TVW2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ACP
Query on ACP

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A
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.051α = 90.00
b = 67.923β = 90.00
c = 83.192γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SHELXL-97refinement
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-07-24
    Type: Data collection, Refinement description