PDBsum entry 2wwh

Transferase

PDB id: 2wwh

Contents

Protein chains

211 a.a. *

Ligands

T5A ×3

Metals

_NA ×5

Waters ×100

* Residue conservation analysis

PDB id:

2wwh

Name:

Transferase

Title:

Plasmodium falciparum thymidylate kinase in complex with ap5dt

Structure:

Thymidilate kinase, putative. Chain: a, b, c. Engineered: yes

Source:

Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.70Å R-factor: 0.191 R-free: 0.270

Authors:

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

Key ref:

J.L.Whittingham et al. (2010). Structural basis for the efficient phosphorylation of AZT-MP (3'-azido-3'-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase. Biochem J, 428, 499-509. PubMed id: 20353400

Date:

23-Oct-09 Release date: 21-Apr-10

Protein chains

Q8I4S1  (Q8I4S1_PLAF7) -  Thymidylate kinase from Plasmodium falciparum (isolate 3D7)

Seq: 210 a.a.

Struc: 211 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.7.4.8 - guanylate kinase.
• Reaction: GMP + ATP = GDP + ADP

GMP (Bound ligand (Het Group name = T5A) matches with 56.36% similarity) + ATP = GDP + ADP

• Enzyme class 3: E.C.2.7.4.9 - dTMP kinase.
• Reaction: dTMP + ATP = dTDP + ADP

dTMP (Bound ligand (Het Group name = T5A) matches with 56.36% similarity) + ATP = dTDP + ADP

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Biochem J 428:499-509 (2010)

PubMed id: 20353400

Structural basis for the efficient phosphorylation of AZT-MP (3'-azido-3'-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase.

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

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.