2.4.2.3: uridine phosphorylase
This is an abbreviated version!
For detailed information about uridine phosphorylase, go to the full flat file.
Word Map on EC 2.4.2.3
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2.4.2.3
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pyrimidine
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nucleoside
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thymidine
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uracil
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5-fluorouracil
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phosphorolysis
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salvage
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orotate
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phosphoribosyltransferase
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phosphorylases
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thymidylate
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fluoropyrimidine
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udp
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5'-deoxy-5-fluorouridine
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5-fluoro-2'-deoxyuridine
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dihydropyrimidine
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acyclonucleoside
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5-fluorouridine
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ribose-1-phosphate
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capecitabine
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5-methyluridine
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dthdpase
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fdurd
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orotidine
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dihydrouracil
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uridine-cytidine
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mete
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diagnostics
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medicine
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synthesis
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drug development
- 2.4.2.3
- pyrimidine
- nucleoside
- thymidine
- uracil
- 5-fluorouracil
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phosphorolysis
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salvage
- orotate
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phosphoribosyltransferase
- phosphorylases
- thymidylate
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fluoropyrimidine
- udp
- 5'-deoxy-5-fluorouridine
- 5-fluoro-2'-deoxyuridine
- dihydropyrimidine
- acyclonucleoside
- 5-fluorouridine
- ribose-1-phosphate
- capecitabine
- 5-methyluridine
- dthdpase
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fdurd
- orotidine
- dihydrouracil
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uridine-cytidine
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mete
- diagnostics
- medicine
- synthesis
- drug development
Reaction
Synonyms
apUP, EC 2.4.2.23, L-UrdPase, More, PcUP1, PcUP2, phosphorylase, uridine, pynpase, pyrimidine nucleoside phosphorylase, pyrimidine phosphorylase, pyrimidine/purine nucleoside phosphorylase, StUPh, udp, UDRPase
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Reaction
Reaction on EC 2.4.2.3 - uridine phosphorylase
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sequential mechanism
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
sequential mechanism
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
sequential mechanism
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
rapid-equilibrium random mechanism
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
ordered bi-bi mechanism
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
ordered bi-bi mechanism
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
random mechanism
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
phosphate binds before uridine and ribose 1-phosphate is released after uracil
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
sequential rather than ping-pong mechanism, addition of substrate is random
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
ordered bi-bi mechanism, phosphate binds before uridine and alpha-D-ribose 1-phosphate is released after uracil
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
binding isotope effects indicate ground-state stabilization in the Michaelis complex, such as bonding environment, ribosyl pucker, and natural bond orbital charges
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
steady-state random kinetic mechanism. Reaction follows an ANDN/SN2 mechanism where chemistry contributes significantly to the overall rate-limiting step of the reaction. No kinetically significant proton transfer step is involved at the transition state. Proton transfer to neutralize the leaving group is not part of transition state formation, consistent with an enzyme-stabilized anionic uracil as the leaving group. Kinetic analysis as a function of pH indicates one protonated group essential for catalysis and for substrate binding
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
mutational analysis supports for the push-pull model of catalysis, proposed catalytic mechanism of PcUP1, modeling, overview. Deprotonation of phosphate by Arg104, increases the negative charge on the phosphate oxygen, leading to repulsion between the electrons of phosphate oxygen and electron pairs of the endocylic ribosyl oxygen and the formation of an intermediate oxocarbenium ion. At the same time, the Gln206, Arg208 and Arg264-N1 hydrogen network-bond pulls electrons from the glycosidic bond onto the pyrimidine ring. These two actions work in concert to weaken the glycosidic bond. Arg39 pivots, to physically push the phosphate closer to the ribose moiety. After glycosidic bond cleavage, ribose-1-phosphate dissociates from the active pocket, and then an active water reprotonates the negatively charged purine. The final step is to release the neutral purine base
uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
rapid-equilibrium random mechanism
Escherichia coli B / ATCC 11303
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uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
mutational analysis supports for the push-pull model of catalysis, proposed catalytic mechanism of PcUP1, modeling, overview. Deprotonation of phosphate by Arg104, increases the negative charge on the phosphate oxygen, leading to repulsion between the electrons of phosphate oxygen and electron pairs of the endocylic ribosyl oxygen and the formation of an intermediate oxocarbenium ion. At the same time, the Gln206, Arg208 and Arg264-N1 hydrogen network-bond pulls electrons from the glycosidic bond onto the pyrimidine ring. These two actions work in concert to weaken the glycosidic bond. Arg39 pivots, to physically push the phosphate closer to the ribose moiety. After glycosidic bond cleavage, ribose-1-phosphate dissociates from the active pocket, and then an active water reprotonates the negatively charged purine. The final step is to release the neutral purine base
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