Steve Ealick's Research Group

Pyrimidine Nucleoside Phosphorylase from Bacillus stearothermophilus

PDB file: 1BRW

Pyrimidine nucleoside phosphorylase (PyNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. In lower organisms (e.g. Bacillus stearothermophilus) PyNP accepts both thymidine and uridine, whereas in mammalian and other higher organisms it is specific for thymidine (and is designated thymidine phosphorylase, TP). PyNP shares 40% sequence similarity (and presumably significant structural similarity) with human TP, which has been implicated as a growth factor in tumor angiogenesis. The crystal structure of PyNP from B. stearothermophilus with the substrate analog pseudouridine in its active site has been solved to 2.1 Å resolution.

This structure confirms the similarity of PyNP to TP and supports the idea of a closed active conformation, which is the result of rigid body movement of the α and α/β domains. The active-site cleft, where the pyrimidine and phosphate substrates bind, is between the two domains.

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The structure reveals an asymmetric dimer in which one subunit is fully closed and the other is only partially closed.


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The schematic drawing of the active-site contacts in subunit B, shows hydrogen bonding with dashed lines and distances in Å. The position of the ribose, which was not experimentally determined, has been modeled.


Pugmire MJ and Ealick SE. The Crystal Structure of Pyrimidine Nucleoside Phosphorylase in a Closed Conformation. Structure 6:1467-1479 (1998).

Zhou M, Pugmire MJ, Vuong BQ, and Ealick SE. Cloning, Expression and Crystallization of Pyrimidine Nucleoside Phosphorylase from Bacillus stearothermophilus. Acta Crystallogr. D 55:287-290 (1999).

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