Steve Ealick's Research Group


Uridine Phosphorylase from Salmonella typhimurium


PDB file:

1RYZ; 2.9 Å

1SJ9; 2.5 Å

1Y1T; 1.77 Å

1Y1S; complex with uracil and sulfate ion

1Y1R; complex with inhibitor and phosphate ion

1Y1Q; complex with uridine-5p-monophosphate and sulfate ion

1ZL2; complex with 2,2′-anhydrouridine and phosphate ion

Description:

Uridine phosphorylase from Salmonella typhimurium (StUP) catalyzes the reversible phosphorolysis of uridine with the formation of ribose-1-phosphate and uracil. The crystals belong to space group P61 with a = 91.37 Å and c = 266.38 Å, and diffract to 2.5 Å resolution.The structure was determined by molecular replacement method using 1RYZ as the search model.

The monomer unit of StUP includes 253 amino acid residues, with a 97% identity to the amino acid sequence of E. coli uridine phosphorylase (EcUP). It is also similar in structure to both human purine nucleoside phosphorylase, E. coli purine nucleoside phosphorylase and Trichomonas vaginalis purine nucleoside phosphorylase. The monomer is shown with phosphate bound in the active site.

 

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The active form of the enzyme is a hexamer of identical subunits with a molecular weight of 165 kDA. The hexameric StUPh displays 32 point group symmetry and utilizes both twofold and threefold non-crystallographic axes. As such, it is structurally homologous to the hexameric purine nucleoside phosphorylases. There are no large conformation changes between the monoclinic and trigonal crystal forms nor between the six subunits in the hexamer.

 

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Open, intermediate and closed active site conformations were described for EcUP based on the position of residues in loop 219-239. The open active site was observed when no substrates were bound and the intermediate and closed active site conformations were found when substrates were bound to the monomers. StUP contains only the open conformation of the active site; therefore, the presence of phosphate ion does not appear to influence the conformational state of the active site loop. This view of the active site shows the orthophosphate bound at the interface of two monomers.

 

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References:

Dontsova MV, Gabdoulkhakov AG, Molchan OK, Lashkov AA, Garber MB, Mironov AS, Zhukhlistova NE, Morgunova EYu, Voelter,W, Betzel C, Zhang Y, Ealick SE and Mikhailov AM. Preliminary Investigation of the Three-dimensional Structure of Salmonella typhimurium Uridine Phosphorylase in the Crystal State. Acta Crystallogr. F. 61:337-340 (2005)



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