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

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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. / Safonova, Tatyana N.; Mikhailov, Sergey N.; Veiko, Vladimir P.; Mordkovich, Nadezhda N.; Manuvera, Valentin A.; Alekseev, Cyril S.; Kovalchuk, Mikhail V.; Popov, Vladimir O.; Polyakov, Konstantin M.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 70, No. 12, 01.12.2014, p. 3310-3319.

Research output: Contribution to journal › Article › peer-review

Author

Safonova, Tatyana N. ; Mikhailov, Sergey N. ; Veiko, Vladimir P. ; Mordkovich, Nadezhda N. ; Manuvera, Valentin A. ; Alekseev, Cyril S. ; Kovalchuk, Mikhail V. ; Popov, Vladimir O. ; Polyakov, Konstantin 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. In: Acta Crystallographica Section D: Biological Crystallography. 2014 ; Vol. 70, No. 12. pp. 3310-3319.

BibTeX

@article{e75eba531b61410085b45be4fe3a082c,

title = "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",

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.",

keywords = "atomic resolution, crystallization under microgravity, high-syn conformation of uridine, Shewanella oneidensis MR-1, twinning, uridine phosphorylase",

author = "Safonova, {Tatyana N.} and Mikhailov, {Sergey N.} and Veiko, {Vladimir P.} and Mordkovich, {Nadezhda N.} and Manuvera, {Valentin A.} and Alekseev, {Cyril S.} and Kovalchuk, {Mikhail V.} and Popov, {Vladimir O.} and Polyakov, {Konstantin M.}",

note = "Publisher Copyright: {\textcopyright} 2014 International Union of Crystallography.",

year = "2014",

month = dec,

day = "1",

doi = "10.1107/S1399004714024079",

language = "English",

volume = "70",

pages = "3310--3319",

journal = "Acta Crystallographica Section F: Structural Biology and Crystallization Communications",

issn = "2053-230X",

publisher = "Wiley-Blackwell",

number = "12",

}

RIS

TY - JOUR

T1 - 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

AU - Safonova, Tatyana N.

AU - Mikhailov, Sergey N.

AU - Veiko, Vladimir P.

AU - Mordkovich, Nadezhda N.

AU - Manuvera, Valentin A.

AU - Alekseev, Cyril S.

AU - Kovalchuk, Mikhail V.

AU - Popov, Vladimir O.

AU - Polyakov, Konstantin M.

PY - 2014/12/1

Y1 - 2014/12/1

N2 - 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.

AB - 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.

KW - atomic resolution

KW - crystallization under microgravity

KW - high-syn conformation of uridine

KW - Shewanella oneidensis MR-1

KW - twinning

KW - uridine phosphorylase

UR - http://www.scopus.com/inward/record.url?scp=84916899357&partnerID=8YFLogxK

U2 - 10.1107/S1399004714024079

DO - 10.1107/S1399004714024079

M3 - Article

C2 - 25478848

AN - SCOPUS:84916899357

VL - 70

SP - 3310

EP - 3319

JO - Acta Crystallographica Section F: Structural Biology and Crystallization Communications

JF - Acta Crystallographica Section F: Structural Biology and Crystallization Communications

SN - 2053-230X

IS - 12

ER -

ID: 88207577