4R2W

X-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 in complex with uridine at 1.6 A resolution

Replaces:  4HER

Summary for 4R2W

• Entry DOI: 10.2210/pdb4r2w/pdb
• Related: 4R2X
• Descriptor: Uridine phosphorylase, SULFATE ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: uridine phosphorylase, uridine binding, transferase
• Biological source: Shewanella oneidensis MR-1
• Total number of polymer chains: 6
• Total formula weight: 162831.35

Authors

Safonova, T.N.,Mordkovich, N.N.,Manuvera, V.A.,Veiko, V.P.,Popov, V.O.,Polyakov, K.P. (deposition date: 2014-08-13, release date: 2014-12-10, Last modification date: 2023-09-20)

Primary citation

Safonova, T.N.,Mikhailov, S.N.,Veiko, V.P.,Mordkovich, N.N.,Manuvera, V.A.,Alekseev, C.S.,Kovalchuk, M.V.,Popov, V.O.,Polyakov, K.M.
High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine.
Acta Crystallogr.,Sect.D, 70:3310-3319, 2014

PubMed Abstract: Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Expression of UP from Shewanella oneidensis MR-1 (SoUP) was performed in Escherichia coli. The high-resolution X-ray structure of SoUP was solved in the free form and in complex with uridine. A crystal of SoUP in the free form was grown under microgravity and diffracted to ultrahigh resolution. Both forms of SoUP contained sulfate instead of phosphate in the active site owing to the presence of ammonium sulfate in the crystallization solution. The latter can be considered as a good mimic of phosphate. In the complex, uridine adopts a high-syn conformation with a nearly planar ribose ring and is present only in one subunit of the hexamer. A comparison of the structures of SoUP in the free form and in complex with the natural substrate uridine showed that the subunits of the hexamer are not identical, with the active sites having either an open or a closed conformation. In the monomers with the closed conformation, the active sites in which uridine is absent contain a glycerol molecule mimicking the ribose moiety of uridine.

PubMed: 25478848
DOI: 10.1107/S1399004714024079

Experimental method

X-RAY DIFFRACTION (1.6 Å)