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Title: Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil

Abstract

The structure of bacterial uridine phosphorylase (UPh) belonging to the NP-I family in complex with 6-methyluracil was determined for the first time at 1.17 Å resolution. The structural features of bacterial UPh from the bacterium Vibrio cholerae (VchUPh) responsible for selectivity toward 6-methyluracil acting as a pseudosubstrate were revealed. The repulsion between the hydrophilic hydroxyl group of the active-site residue Thr93 of VchUPh and the hydrophobic methyl group of 6-methyluracil prevents the oxygen atom O4' of the ribose moiety and the phosphate oxygen atom O3P of ribose 1-phosphate from forming hydrogen bonds with OG1-Thr93, which are essential for the enzymatic reaction. This, apparently, makes VchUPh inactive in the enzymatic synthesis of 6-methyluridine from 6-methyluracil. Hence, Thr93 is the residue, the modification of which will allow VchUPh to catalyze the biotechnologically important synthesis of 6-methyluridine from 6-methyluracil. Taking into account high structural homology of the functionally significant regions of bacterial UPhs, this conclusion is also true for other bacterial UPhs. It was demonstrated that bacterial thymidine phosphorylases of the NP-II family cannot bind 6-methyluracil in a proper conformation required for the catalysis because of a close contact between the 6-methyl group and Phe210.

Authors:
; ; ;  [1];  [2];  [3];  [1]
  1. Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation)
  2. State Research Institute of Genetics and Selection of Industrial Microorganisms (Russian Federation)
  3. University of Hamburg (Germany)
Publication Date:
OSTI Identifier:
22758237
Resource Type:
Journal Article
Journal Name:
Crystallography Reports
Additional Journal Information:
Journal Volume: 63; Journal Issue: 3; Other Information: Copyright (c) 2018 Pleiades Publishing, Inc.; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 1063-7745
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 60 APPLIED LIFE SCIENCES; ATOMS; BACTERIA; BIOTECHNOLOGY; CATALYSIS; FUNCTIONAL ANALYSIS; HYDROGEN; HYDROXIDES; OXYGEN; PHOSPHATES; PHOSPHOTRANSFERASES; RESIDUES; RESOLUTION; RIBOSE; SYNTHESIS; THYMIDINE; URIDINE

Citation Formats

Prokofev, I. I., E-mail: prokoigor@mail.com, Lashkov, A. A., Gabdulkhakov, A. G., Balaev, V. V., Mironov, A. S., Betzel, C., and Mikhailov, A. M. Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil. United States: N. p., 2018. Web. doi:10.1134/S1063774518030239.
Prokofev, I. I., E-mail: prokoigor@mail.com, Lashkov, A. A., Gabdulkhakov, A. G., Balaev, V. V., Mironov, A. S., Betzel, C., & Mikhailov, A. M. Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil. United States. doi:10.1134/S1063774518030239.
Prokofev, I. I., E-mail: prokoigor@mail.com, Lashkov, A. A., Gabdulkhakov, A. G., Balaev, V. V., Mironov, A. S., Betzel, C., and Mikhailov, A. M. Tue . "Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil". United States. doi:10.1134/S1063774518030239.
@article{osti_22758237,
title = {Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil},
author = {Prokofev, I. I., E-mail: prokoigor@mail.com and Lashkov, A. A. and Gabdulkhakov, A. G. and Balaev, V. V. and Mironov, A. S. and Betzel, C. and Mikhailov, A. M.},
abstractNote = {The structure of bacterial uridine phosphorylase (UPh) belonging to the NP-I family in complex with 6-methyluracil was determined for the first time at 1.17 Å resolution. The structural features of bacterial UPh from the bacterium Vibrio cholerae (VchUPh) responsible for selectivity toward 6-methyluracil acting as a pseudosubstrate were revealed. The repulsion between the hydrophilic hydroxyl group of the active-site residue Thr93 of VchUPh and the hydrophobic methyl group of 6-methyluracil prevents the oxygen atom O4' of the ribose moiety and the phosphate oxygen atom O3P of ribose 1-phosphate from forming hydrogen bonds with OG1-Thr93, which are essential for the enzymatic reaction. This, apparently, makes VchUPh inactive in the enzymatic synthesis of 6-methyluridine from 6-methyluracil. Hence, Thr93 is the residue, the modification of which will allow VchUPh to catalyze the biotechnologically important synthesis of 6-methyluridine from 6-methyluracil. Taking into account high structural homology of the functionally significant regions of bacterial UPhs, this conclusion is also true for other bacterial UPhs. It was demonstrated that bacterial thymidine phosphorylases of the NP-II family cannot bind 6-methyluracil in a proper conformation required for the catalysis because of a close contact between the 6-methyl group and Phe210.},
doi = {10.1134/S1063774518030239},
journal = {Crystallography Reports},
issn = {1063-7745},
number = 3,
volume = 63,
place = {United States},
year = {2018},
month = {5}
}