Structure ofEscherichia coliuridine phosphorylase at 2.0 Å

Abstract

The 2.0 Å crystal structure has been determined for Escherichia coli uridine phosphorylase (UP), an essential enzyme in nucleotide biosynthesis that catalyzes the phosphorolytic cleavage of the C—N glycosidic bond of uridine to ribose‐1‐phosphate and uracil. The structure determination of two independent monomers in the asymmetric unit revealed the residue composition and atomic details of the apo configurations of each active site. The native hexameric UP enzyme was revealed by applying threefold crystallographic symmetry to the contents of the asymmetric unit. The 2.0 Å model reveals a closer structural relationship to other nucleotide phosphorylase enzymes than was previously appreciated.

Crystal Structures of Escherichia coli Uridine Phosphorylase in Two Native and Three Complexed Forms Reveal Basis of Substrate Specificity, Induced Conformational Changes and Influence of Potassium

“…The two native structures are both in the R3 (H3) space group and are termed Type-A and Type-B. The Type-A native structure determined at 2.2 Å resolution is essentially identical with that reported by Burling et al, 12 with a dimer in the asymmetric unit containing one fully ordered monomer while the other monomer has the loop regions 163 -183, and 222 -232 disordered. The Type-B UP structure was crystallized under the same conditions as the Type-A structure except that potassium acetate was substituted for sodium acetate.…”

“…10 There are presently three E. coli UP structures deposited in the Protein Data Bank (1K3F, 11 1LGG (CaradocDavies et al, this work 2002), 1LX7 12 ). The structures of two NP-II family members, thymidine phosphorylase from E. coli, 13,14 and pyrimidine phosphorylase from Bacillus stearothermophilus, 15 have also been published.…”

The Three-dimensional Structure of the N-Acetylglucosamine-6-phosphate Deacetylase, NagA, from Bacillus subtilis

“…The 180°-rotational symmetry between two monomers of granzymeA is used in the functional dimer to form an extended substrate-binding cleft (31,32). Examples of an Arg residue cooperating (from adjacent subunits in a hexamer) to ligate a substrate phosphate ion include uridine phosphorylase (33) and purine nucleoside phosphorylase (34).…”

Crystal Structure of Purine Nucleoside Phosphorylase from Thermus thermophilus

“…21 -23 Also, some of the pyrimidine nucleoside phosphorylases (PyNPs), e.g. uridine phosphorylase from E. coli, 24,25 appear to be similar to the hexameric PNPs.…”