Steve Ealick's Research Group

Bovine Uridine Phosphorylase

PDB files:

3KU4, native

3KVY, complexed with uracil, a trapped glycal and sulfate

3KVR, complexed with 5-fluorouracil, a trapped glycal and sulfate

3KUK, complexed with 2-deoxyuridine


Bovine uridine phosphorylase (bUP) catalyzes the reversible phosphorolysis of uridine with the formation of ribose-1-phosphate and uracil. We have previously determined the structures of Escherichia coli UP (EcUP) and Salmonella typhimurium UP (StUP) and were interested in comparing the bacterial enzyme to the mammalian enzyme.

Even though the sequence similarity is low, the basic topology is the same for EcUP, StUP and bUP and the residues of the active site are conserved. bUP has 27 additional residues at the N-terminal and consequently extra structural features.

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While EcUP and StUP are hexamers (trimer of dimers), bUP exists a dimer. The extra residues are expected to be the cause of the difference in assembly, since they both add extra stability to the dimer interface and provide a long loop that might interfere with crystal contacts.


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Of particular interest in the active site of UP is the capture of a glycal, thought to be an oxocarbenium ion intermediate, sandwiched between the uridine or fluorouridine and sulfate binding sites crystals prepared with those reagents.

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Paul D, O’Leary SE, Rajashankar KR, Bu W, Toms AV, Settembre EC, Sander JM, Begley TP and Ealick SE. Glycal Formation in Crystals of Uridine Phosphorylase. Biochemistry 49, 3499-3509. (2010) PubMed

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