2WWF

Plasmodium falciparum thymidylate kinase in complex with TMP and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Efficient Phosphorylation of Aztmp and Dgmp by Plasmodium Falciparum Type I Thymidylate Kinase.

Whittingham, J.L.Carrero-Lerida, J.Brannigan, J.A.Ruiz-Perez, L.M.Silva, A.P.G.Fogg, M.J.Wilkinson, A.J.Gilbert, I.H.Wilson, K.S.Gonzalez-Pacanowska, D.

(2010) Biochem J 428: 499

  • DOI: 10.1042/BJ20091880
  • Primary Citation of Related Structures:  
    2WWF, 2WWG, 2WWH, 2WWI

  • PubMed Abstract: 
  • Plasmodium falciparum is the causative agent of malaria, a disease where new drug targets are required due to increasing resistance to current anti-malarials. TMPK (thymidylate kinase) is a good candidate as it is essential for the synthesis of dTTP, a critical precursor of DNA and has been much studied due to its role in prodrug activation and as a drug target ...

    Plasmodium falciparum is the causative agent of malaria, a disease where new drug targets are required due to increasing resistance to current anti-malarials. TMPK (thymidylate kinase) is a good candidate as it is essential for the synthesis of dTTP, a critical precursor of DNA and has been much studied due to its role in prodrug activation and as a drug target. Type I TMPKs, such as the human enzyme, phosphorylate the substrate AZT (3'-azido-3'-deoxythymidine)-MP (monophosphate) inefficiently compared with type II TMPKs (e.g. Escherichia coli TMPK). In the present paper we report that eukaryotic PfTMPK (P. falciparum TMPK) presents sequence features of a type I enzyme yet the kinetic parameters for AZT-MP phosphorylation are similar to those of the highly efficient E. coli enzyme. Structural information shows that this is explained by a different juxtaposition of the P-loop and the azide of AZT-MP. Subsequent formation of the transition state requires no further movement of the PfTMPK P-loop, with no steric conflicts for the azide moiety, allowing efficient phosphate transfer. Likewise, we present results that confirm the ability of the enzyme to uniquely accept dGMP as a substrate and shed light on the basis for its wider substrate specificity. Information resulting from two ternary complexes (dTMP-ADP and AZT-MP-ADP) and a binary complex with the transition state analogue AP5dT [P1-(5'-adenosyl)-P5-(5'-thymidyl) pentaphosphate] all reveal significant differences with the human enzyme, notably in the lid region and in the P-loop which may be exploited in the rational design of Plasmodium-specific TMPK inhibitors with therapeutic potential.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO105YW, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDILATE KINASE, PUTATIVEA, B, C212Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1251300
EC: 2.7.4.9
UniProt
Find proteins for Q8I4S1 (Plasmodium falciparum (isolate 3D7))
Explore Q8I4S1 
Go to UniProtKB:  Q8I4S1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A], M [auth B], U [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
TMP (Subject of Investigation/LOI)
Query on TMP

Download Ideal Coordinates CCD File 
D [auth A], L [auth B], T [auth C]THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , P [auth B] , Q [auth B] , R [auth B] , S [auth B] , X [auth C] , 
H [auth A],  I [auth A],  J [auth A],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  X [auth C],  Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], K [auth A], N [auth B], O [auth B], V [auth C], W [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.127α = 90
b = 110.127β = 90
c = 120.097γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Non-polymer description, Structure summary, Version format compliance