4LHM

Thymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine

Summary for 4LHM

• Entry DOI: 10.2210/pdb4lhm/pdb
• Descriptor: Thymidine phosphorylase, SULFATE ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 48364.86

Authors

Timofeev, V.I.,Abramchik, Y.A.,Esipov, R.S.,Kuranova, I.P. (deposition date: 2013-07-01, release date: 2014-04-09, Last modification date: 2024-02-28)

Primary citation

Timofeev, V.,Abramchik, Y.,Zhukhlistova, N.,Muravieva, T.,Fateev, I.,Esipov, R.,Kuranova, I.
3'-Azidothymidine in the active site of Escherichia coli thymidine phosphorylase: the peculiarity of the binding on the basis of X-ray study.
Acta Crystallogr.,Sect.D, 70:1155-1165, 2014

PubMed Abstract: The structural study of complexes of thymidine phosphorylase (TP) with nucleoside analogues which inhibit its activity is of special interest because many of these compounds are used as chemotherapeutic agents. Determination of kinetic parameters showed that 3'-azido-3'-deoxythymidine (3'-azidothymidine; AZT), which is widely used for the treatment of human immunodeficiency virus, is a reversible noncompetitive inhibitor of Escherichia coli thymidine phosphorylase (TP). The three-dimensional structure of E. coli TP complexed with AZT was solved by the molecular-replacement method and was refined at 1.52 Å resolution. Crystals for X-ray study were grown in microgravity by the counter-diffusion technique from a solution of the protein in phosphate buffer with ammonium sulfate as a precipitant. The AZT molecule was located with full occupancy in the electron-density maps in the nucleoside-binding pocket of TP, whereas the phosphate-binding pocket of the enzyme was occupied by phosphate (or sulfate) ion. The structure of the active-site cavity and conformational changes of the enzyme upon AZT binding are described in detail. It is found that the position of AZT differs remarkably from the positions of the pyrimidine bases and nucleoside analogues in other known complexes of pyrimidine phosphorylases, but coincides well with the position of 2'-fluoro-3'-azido-2',3'-dideoxyuridine (N3FddU) in the recently investigated complex of E. coli TP with this ligand (Timofeev et al., 2013). The peculiarities of the arrangement of N3FddU and 3'-azidothymidine in the nucleoside binding pocket of TP and correlations between the arrangement and inhibitory properties of these compounds are discussed.

PubMed: 24699659
DOI: 10.1107/S1399004714001904

Experimental method

X-RAY DIFFRACTION (1.52 Å)