Steve Ealick's Research Group

Uridine Phosphorylase from E. coli

PDB file:

*1K3F(monoclinic form)

#1U1C UDP-BAU 5-(benzyl)acyclouridine

#1U1D UDP-PTAU 5-(phenylthio)acyclouridine

#1U1E UDP-PSAU 5-(phenylseleno)acyclouridine

#1U1F UDP-BBAU 5-(m-(benzyloxy)benzyl)acyclouridine

#1U1G UDP-BBBA 5-(m-(benzyloxy)benzyl)barbituric acid

1TGV UDP complexed with 5-fluorouridine and sulfate

1TGY UDP complexed with uracil and ribose 1-phosphate

&3KVV UDP complexed with 5-fluorouridine and sulfate


Uridine phosphorylase from E. coli (Upase) catalyzes the reversible phosphorolysis of uridine with the formation of ribose-1-phosphate and uracil. The enzyme had previously been crystallized in a triclinic form. It has now been crystallized, using the vapor diffusion technique, in a new monoclinic crystal form. The structure was determined by the molecular replacement method at 2.5 Å resolution.

The monomer unit of Upase includes 253 amino acid residues. It is similar in structure to both human purine nucleoside phosphorylase and E. coli purine nucleoside phosphorylase.


Click the image to enlarge.


The active form of the enzyme is a hexamer of identical subunits with a molecular weight of 165 kDA and. There are no large conformation changes between the monoclinic and trigonal crystal forms nor between the six subunits in the hexamer.


Click the image to enlarge.

The active site is near the interface of two subunits. The residues at the pyrimidine binding site are shown in one schematic diagram; while the residues at the phosphate binding site are shown in another.


Cook WJ, Koszalka GW, Hall WW, Narayana SVL, and Ealick SE. Crystallization and Preliminary X-ray Investigation of Uridine Phosphorylase from Escherichia coli. J. Biol. Chem. 262(6):2852-2853 (1987).

Morgunova, EYu, Mikhailov AM, Komissarov AA, Mao C, Lin'kova EV, Mironov AS, Popov AN, Armstrong S, Burlakova AA, Romanova DV, Blagova EV, Smirnova EA, Debabov VG, Ealick SE. Structural-functional aspect of the investigation of the molecular structure of uridine phosphorylase from E. coli. Crystallography Reports 40:620-628 (1995).

*Morgunova EU, Mikhailov AM, Popov AN, Blagova EV, Smirnova EA, Vainshtein, KB, Mao C, Armstrong SR, Ealick SE, Komissarov AA, Linkova EV, Burlakova AA, Mironov AS, Debabov,VG. Atomic Structure at 2.5 Å Resolution of Uridine Phosphorylase from E. coli as Refined in the Monoclinic Crystal Lattice. FEBS Lett. 367(2):183-187 (1995).

# Bu W, Settembre EC, el Kouni MH, and Ealick SE. Structural Basis for Inhibition of Escherichia coli Uridine Phosphorylase by 5-substituted Acyclouridines. Acta Crystallogr. D. 61:863-872 (2005).

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

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