Steve Ealick's Research Group

Nucleoside 2-Deoxyribosyltransferase

PDB file:

1F8X (native)

1F8Y (with substrate analog 5-methyl-2′-deoxypseudoridine (5mΨU))


Nucleoside 2-deoxyribosyltransferase (NDT) plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of β-2′-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. We describe the crystal structure of the enzyme with and without bound ligand. The native structure was solved by the single isomorphous replacement with anomalous scattering method (SIRAS) and refined to 2.5 Å resolution resulting in a crystallographic R factor of 16.6%.

The NDT monomer fold is a single doubly-wound α/β domain; it also exhibits a unique nucleoside-binding motif. The core of the molecule consists of a central parallel five-stranded β-sheet, flanked by four α-helices. This drawing shows the NDT subunit with the substrate analog 5-methyl-2′-deoxypseudoridine (5mYU) shown as a ball-and-stick model.


Click the image to enlarge.


The native enzyme consists of a "trimer of dimers", which are viewed here down the crystallographic three-fold axis. X-ray analysis of enzyme-purine and enzyme-pyrimidine complexes reveals that the active site lies in a cleft formed by the edge of the β-sheet and two α-helices and contains side chains from two subunits. The substrate analog 5mΨU is shown with ball-and-stick modeling to illustrate the way in which two subunits interact to form the active site.


Click the image to enlarge.



Armstrong SR, Cook WJ, Short SA and Ealick SE. Crystal Structures of Nucleoside Deoxyribosyltransferase in Native and Ligand-Bound Forms Reveal Architecture of the Active Site. Structure 4:97-107 (1996).

Short SA, Armstrong SR, Ealick SE and Porter DJT. Active Site Amino Acids That Participate in the Catalytic Mechanism of Nucleoside 2′'-Deoxyribosyltransferase. J. Biol. Chem. 271:4978-4987 (1996).

Cook WJ, Short SA, and Ealick SE. Crystallization and Preliminary X-ray Investigation of Recombinant Lactobacillus leichmanni Nucleoside Deoxyribosyltransferase, J. Biol. Chem. 265(5):2682-2683 (1990).

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