Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.69 kDa 
• Atom Count: 5,654 
• Modelled Residue Count: 629 
• Deposited Residue Count: 636 
• Unique protein chains: 1

 2WWG

Plasmodium falciparum thymidylate kinase in complex with dGMP and ADP

• PDB DOI: 10.2210/pdb2WWG/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-23 Released: 2010-04-21 
• Deposition Author(s): Whittingham, J.L., Carrero-Lerida, J., Brannigan, J.A., Ruiz-Perez, L.M., Silva, A.P., Fogg, M.J., Wilkinson, A.J., Gilbert, I.H., Wilson, K.S., Gonzalez-Pacanowska, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.258 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

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., Fogg, M.J., Wilkinson, A.J., Gilbert, I.H., Wilson, K.S., Gonzalez-Pacanowska, D.

(2010) Biochem J 428: 499

• PubMed: 20353400 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDILATE KINASE, PUTATIVE	A, B, C	212	Plasmodium falciparum 3D7	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	AA [auth C], E [auth A], Q [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
DGP	D [auth A], P [auth B], Z [auth C]	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P LTFMZDNNPPEQNG-KVQBGUIXSA-N
GOL	DA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	BA [auth C], CA [auth C], F [auth A], G [auth A], R [auth B], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.258 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.741	α = 90
b = 110.741	β = 90
c = 119.361	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Whittingham, J.L., Carrero-Lerida, J., Brannigan, J.A., Ruiz-Perez, L.M., Silva, A.P., Fogg, M.J., Wilkinson, A.J., Gilbert, I.H., Wilson, K.S., Gonzalez-Pacanowska, D.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2013-03-13
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary