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Information on EC 2.4.2.2 - pyrimidine-nucleoside phosphorylase
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2.4.2.2 pyrimidine-nucleoside phosphorylaseIUBMB Comments
Unlike EC 2.4.2.3, uridine phosphorylase, and EC 2.4.2.4, thymidine phosphorylase, this enzyme can accept both the ribonucleosides uridine and cytidine and the 2'-deoxyribonucleosides 2'-deoxyuridine and thymidine [3,6]. The reaction is reversible, and the enzyme does not distinguish between alpha-D-ribose 1-phosphate and 2-deoxy-alpha-D-ribose 1-phosphate in the synthetic direction.
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Word Map
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
nucleoside phosphorylase, pynp, bbpynp, py-npase, ttpynp, ttha1771, pyrimidine-nucleoside phosphorylase, pyrimidine ribonucleoside phosphorylase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AmPyNP
BbPyNP
BsPyNP
deoA
EC 2.4.2.23
-
-
formerly, part transferred
-
PDP
phosphorylase, pyrimidine nucleoside
-
-
-
-
Py-NPase
PYNP
pynpase
pyrimidine nucleoside phosphorylase
pyrimidine ribonucleoside phosphorylase
-
-
-
-
TTHA1771
Py-NPase
-
-
-
-
PYNP
-
-
-
-
pynpase
-
-
-
-
pyrimidine nucleoside phosphorylase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2'-deoxyuridine + phosphate = uracil + 2-deoxy-alpha-D-ribose 1-phosphate
(3)
-
-
-
cytidine + phosphate = cytosine + alpha-D-ribose 1-phosphate
(2)
-
-
-
thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate
(4)
-
-
-
uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
(1)
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pentosyl group transfer
pentosyl group transfer
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
pyrimidine-nucleoside:phosphate (2'-deoxy)-alpha-D-ribosyltransferase
Unlike EC 2.4.2.3, uridine phosphorylase, and EC 2.4.2.4, thymidine phosphorylase, this enzyme can accept both the ribonucleosides uridine and cytidine and the 2'-deoxyribonucleosides 2'-deoxyuridine and thymidine [3,6]. The reaction is reversible, and the enzyme does not distinguish between alpha-D-ribose 1-phosphate and 2-deoxy-alpha-D-ribose 1-phosphate in the synthetic direction.
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CAS REGISTRY NUMBER
COMMENTARY
9055-35-0
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose 1-phosphate
1,2,4-triazole-3-carboxamide + alpha-D-ribose 1-phosphate
ribavirin + phosphate
-
-
-
-
?
2'-C-methyluridine + phosphate
uracil + 2-C-methyl-alpha-D-ribose 1-phosphate
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
2'-deoxy-2'-fluorouridine + phosphate
?
-
-
poor activity, 0.4% substrate conversion after 30 min
-
?
2'-deoxy-2'-fluorouridine + phosphate
uracil + 2-deoxy-2-fluoro-alpha-D-ribose 1-phosphate
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
2'-deoxyuridine + 5-bromovinyluracil
(E)-5-(2-bromovinyl)-2'-deoxyuridine + uracil
-
-
-
-
?
2'-deoxyuridine + 5-fluorouracil
5-fluoro-2'-deoxyuridine + uracil
-
-
-
-
?
2'-deoxyuridine + 5-trifluoromethyluracil
5-trifluoromethyl-2'-deoxyuridine + uracil
-
-
-
-
?
2,6-dichloropurine 2'-deoxyriboside + phosphate
?
-
-
-
r
3'-C-methyluridine + phosphate
uracil + 3-C-methyl-alpha-D-ribose 1-phosphate
-
-
-
r
3'-fluoro-3'-deoxyuridine + phosphate
uracil + 3'-fluoro-3'-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
4-thiothymidine + phosphate
4-thiothymine + alpha-D-ribose 1-phosphate
-
uridine phosphorylase activity, see also EC 2.4.2.3
-
-
r
5'-azido-5'-deoxythymidine + phosphate
thymine + 5-azido-5-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
5'-bromo-5'-deoxythymidine + phosphate
thymine + 5-bromo-5-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
5'-chloro-5'-deoxythymidine + phosphate
thymine + 5'-chloro-5'-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
5'-deoxy-5'-methyleneuridine + phosphate
uracil + 5-deoxy-5'-methylene-alpha-D-ribose 1-phosphate
-
-
-
r
5'-deoxy-5-fluorouridine + phosphate
5-fluorouracil + alpha-D-deoxyribose 1-phosphate
-
-
5-fluorouracil is a chemotherapeutic agent and inactivated by dihydropyrimidine dihydrogenase activity
-
?
5'-deoxythymidine + phosphate
thymine + 5-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
5'-homothymidine + phosphate
thymine + 5-homo-alpha-D-ribose 1-phosphate
-
-
-
r
5'-homouridine + phosphate
uracil + 5-homo-alpha-D-ribose 1-phosphate
-
-
-
r
5'-iodo-5'-deoxythymidine + phosphate
thymine + 5-iodo-5-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
5-bromodeoxyuridine + phosphate
5-bromouracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
5-C-methyluridine + phosphate
5-C-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-chlorodeoxyuridine + phosphate
5-chlorouracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
5-fluorodeoxyuridine + phosphate
5-fluorouracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
5-fluorouridine + phosphate
5-fluorouracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
5-iododeoxyuridine + phosphate
5-iodouracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
5-iodouridine + phosphate
5-iodouracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
5-trifluoromethyl-2'-deoxyuridine + phosphate
5-trifluoromethyluracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
6-chloro-2-fluoropurine 2'-deoxyriboside + phosphate
?
-
-
-
r
6-methyluridine + phosphate
6-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
alpha-D-ribose 1-phosphate + uracil
phosphate + uridine
-
-
-
?
phosphate + uridine
alpha-D-ribose 1-phosphate + uracil
-
-
-
r
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
thymidine + phosphate
-
-
-
r
uracil arabinoside + phosphate
uracil + alpha-D-arabinose 1-phosphate
-
-
-
-
?
(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose 1-phosphate
-
1.6% substrate conversion after 30 min
-
?
(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose 1-phosphate
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
-
1.6% substrate conversion after 30 min
-
?
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
-
-
-
r
2'-deoxy-2'-fluorouridine + phosphate
uracil + 2-deoxy-2-fluoro-alpha-D-ribose 1-phosphate
-
15.6% substrate conversion after 30 min
-
?
2'-deoxy-2'-fluorouridine + phosphate
uracil + 2-deoxy-2-fluoro-alpha-D-ribose 1-phosphate
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
-
15.6% substrate conversion after 30 min
-
?
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
-
-
-
r
2'-deoxythymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
2'-deoxythymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
2'-deoxythymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
2'-deoxyuridine + phosphate
uracil + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
2'-deoxyuridine + phosphate
uracil + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
?
2'-deoxyuridine + phosphate
uracil + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
4-thiouridine + phosphate
4-thiouracil + alpha-D-ribose 1-phosphate
-
-
-
r
4-thiouridine + phosphate
4-thiouracil + alpha-D-ribose 1-phosphate
-
thymidine phosphorylase activity, see also EC 2.4.2.4
-
-
r
5'-deoxyuridine + phosphate
uracil + 5-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
5'-deoxyuridine + phosphate
uracil + 5-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-thymidine + phosphate
5-bromo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-thymidine + phosphate
5-bromo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-thymidine + phosphate
5-bromo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-uridine + phosphate
5-bromo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-uridine + phosphate
5-bromo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-uridine + phosphate
5-bromo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromodeoxyuridine + phosphate
5-bromouracil + deoxyribose 1-phosphate
-
95% of the activity with uridine
-
-
?
5-bromodeoxyuridine + phosphate
5-bromouracil + deoxyribose 1-phosphate
-
-
-
-
?
5-bromodeoxyuridine + phosphate
5-bromouracil + deoxyribose 1-phosphate
-
74% of the activity with uridine
-
-
?
5-bromouridine + phosphate
5-bromouracil + alpha-D-ribose 1-phosphate
-
95% of the activity with uridine
-
-
?
5-bromouridine + phosphate
5-bromouracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
5-bromouridine + phosphate
5-bromouracil + alpha-D-ribose 1-phosphate
-
40% of the activity with uridine
-
-
?
5-fluoro-2'-deoxyuridine + phosphate
5-fluorouracil + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
?
5-fluoro-2'-deoxyuridine + phosphate
5-fluorouracil + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
?
5-iodo-thymidine + phosphate
5-iodo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-thymidine + phosphate
5-iodo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-thymidine + phosphate
5-iodo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-uridine + phosphate
5-iodo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-uridine + phosphate
5-iodo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-uridine + phosphate
5-iodo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
?
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
?
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
27% of the activity with uridine
-
-
?
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-trifluorothymidine + phosphate
5-trifluorothymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
5-trifluorothymidine + phosphate
5-trifluorothymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
cytidine + phosphate
cytosine + alpha-D-ribose 1-phosphate
-
8% of the activity with uridine
-
-
?
cytidine + phosphate
cytosine + alpha-D-ribose 1-phosphate
-
no activity
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
2'-deoxyuridine
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
179% of the activity with uridine, by measuring the conversion of uracil to uridine or deoxyuridine a slight preference for ribose 1-phosphate over deoxyribose 1-phosphate is observed
-
-
r
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
2'-deoxyuridine
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
12% of the activity with uridine
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
147% of the activity with uridine
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
147% of the activity with uridine
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
-
-
-
?
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
-
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
ribofuranosyl thymine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
-
?
ribofuranosyl thymine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
r
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
139% of the activity with uridine
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
21% of the activity with uridine
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
99% of the activity with uridine
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
99% of the activity with uridine
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
-
-
-
?
thymidine + phosphate
thymine + alpha-D-deoxyribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + alpha-D-deoxyribose 1-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-
r
thymidine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
r
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
r
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
by measuring the conversion of uracil to uridine or deoxyuridine a slight preference for ribose 1-phosphate over deoxyribose 1-phosphate is observed
-
r
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
preferred substrate
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
prefered substrate
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
r
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
prefered substrate
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
preferred substrate
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
prefered substrate
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
prefered substrate
-
-
?
additional information
?
-
the function of His82, Arg169, and Lys188 is to stabilize the uridine in a high-energy conformation by means of electrostatic interactions. These residues are involved in catalysis. The function of Asp162 is likely to activate Lys188 for phosphorolytic catalysis through polarization effects
-
-
?
additional information
?
-
-
the function of His82, Arg169, and Lys188 is to stabilize the uridine in a high-energy conformation by means of electrostatic interactions. These residues are involved in catalysis. The function of Asp162 is likely to activate Lys188 for phosphorolytic catalysis through polarization effects
-
-
?
additional information
?
-
-
the enzyme does not accept arabinonucleosides and 2',3'-dideoxynucleosides as substrates
-
-
?
additional information
?
-
pyrimidine-nucleoside phosphorylase catalyzes the phosphorolytic cleavage of thymidine and uridine with equal activity
-
-
-
additional information
?
-
-
pyrimidine-nucleoside phosphorylase catalyzes the phosphorolytic cleavage of thymidine and uridine with equal activity
-
-
-
additional information
?
-
under preliminary optimized conditions, the biosynthesis of various 5-halogenated pyrimidine nucleosides by BbPyNP reaches the yield of 61-84%. No activity with arauridine, 2',3'-deoxyuridine, cytidine, or deoxycytidine
-
-
-
additional information
?
-
-
under preliminary optimized conditions, the biosynthesis of various 5-halogenated pyrimidine nucleosides by BbPyNP reaches the yield of 61-84%. No activity with arauridine, 2',3'-deoxyuridine, cytidine, or deoxycytidine
-
-
-
additional information
?
-
under preliminary optimized conditions, the biosynthesis of various 5-halogenated pyrimidine nucleosides by BbPyNP reaches the yield of 61-84%. No activity with arauridine, 2',3'-deoxyuridine, cytidine, or deoxycytidine
-
-
-
additional information
?
-
-
predictive profiling of 5-fluorouracil resistance in human cancer cells, overview
-
-
?
additional information
?
-
kinetic constants of the phosphorolysis reaction of uridine derivatives modified at 2'-, 3'- and 5'-positions of the sugar moiety and 2-, 4-, 5- and 6-positions of the heterocyclic base are determined. The absence of the 2'- or 5'-hydroxyl group is not crucial for successful binding and phosphorolysis. On the other hand, absence of both the 2'- and 5'-hydroxyl groups leads to loss of substrate binding to the enzyme. Substrate specificity, overview. 2,2'-O-Anhydrouridine, that models the high-syn conformation of uridine, binds better to the enzyme than uridine, despite the absence of a proton in the 3-position of the heterocyclic base, thus playing an important role in the substrate binding. In this case, the orientation of the heterocycle substantially outweighs the contribution of hydrogen bonding by the 2'-hydroxyl and 3-NH groups in the active site of enzyme UP. This strongly suggests that the 2-oxo group is located quite close to 2'-H in the substrate-UP complex. This is in line with the lack of substrate properties of 2-thiouridine
-
-
-
additional information
?
-
-
no activity with deoxycytidine
-
-
?
additional information
?
-
-
reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway
-
-
?
additional information
?
-
thermophilic PNPs and PyNPs accept nucleosides with arabinose, C2'-fluororibose and C2'-fluoroarabinose as the sugar moiety. Substrate spectrum of thermostable nucleoside phosphorylases, overview
-
-
-
additional information
?
-
-
no substrate: cytidine, deoxycytidine, 2',2'-difluoro-2'-deoxycytidine, 2',2'-difluoro-2'-deoxyuridine, uracil arabinoside, thymine arabinoside, (E)-5-(2-bromovinyl)-deoxyuridine, azidothymidine, stavudine, 6-azauridine
-
-
?
additional information
?
-
-
the enzyme also displays (2'-deoxy)ribosyltransferase activity
-
-
?
additional information
?
-
-
the enzyme also displays (2'-deoxy)ribosyltransferase activity
-
-
?
additional information
?
-
thermophilic PNPs and PyNPs accept nucleosides with arabinose, C2'-fluororibose and C2'-fluoroarabinose as the sugar moiety. Substrate spectrum of thermostable nucleoside phosphorylases, overview
-
-
-
additional information
?
-
no substrate: cytidine, deoxycytidine, adenosine, inosine, or guanosine
-
-
?
additional information
?
-
-
no substrate: cytidine, deoxycytidine, adenosine, inosine, or guanosine
-
-
?
additional information
?
-
thermophilic PNPs and PyNPs accept nucleosides with arabinose, C2'-fluororibose and C2'-fluoroarabinose as the sugar moiety. Substrate spectrum of thermostable nucleoside phosphorylases, overview
-
-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
2'-deoxyuridine + phosphate
uracil + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
alpha-D-ribose 1-phosphate + uracil
phosphate + uridine
-
-
-
?
phosphate + uridine
alpha-D-ribose 1-phosphate + uracil
-
-
-
r
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
thymidine + phosphate
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
-
-
-
r
2'-deoxy-2'-fluoro-beta-D-ribofuranosyl-uracil + phosphate
uracil + 2-deoxy-2-fluoro-beta-D-ribofuranose
-
-
-
r
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
-
-
-
r
2'-deoxy-beta-D-arabinofuranosyl-uracil + phosphate
uracil + 2-deoxy-beta-D-arabinofuranose
-
-
-
r
2'-deoxythymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
2'-deoxythymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
2'-deoxythymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-thymidine + phosphate
5-bromo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-thymidine + phosphate
5-bromo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-thymidine + phosphate
5-bromo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-uridine + phosphate
5-bromo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-uridine + phosphate
5-bromo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-bromo-uridine + phosphate
5-bromo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-thymidine + phosphate
5-iodo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-thymidine + phosphate
5-iodo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-thymidine + phosphate
5-iodo-thymine + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-uridine + phosphate
5-iodo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-uridine + phosphate
5-iodo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-iodo-uridine + phosphate
5-iodo-uracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
-
-
-
r
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
-
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
r
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
-
?
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + 2-deoxy-alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
r
thymidine + phosphate
thymine + alpha-D-ribose 1-phosphate
-
-
-
r
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
r
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
-
-
-
r
additional information
?
-
-
predictive profiling of 5-fluorouracil resistance in human cancer cells, overview
-
-
?
additional information
?
-
-
reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway
-
-
?
additional information
?
-
-
the enzyme also displays (2'-deoxy)ribosyltransferase activity
-
-
?
additional information
?
-
-
the enzyme also displays (2'-deoxy)ribosyltransferase activity
-
-
?
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3,5-bis-(4-chlorobenzoyl)-alpha-D-ribose 1-phosphate
-
competitive inhibition with regard to inosine
uridine
-
above 15 mM, competitive inhibition of cleavage of 5-bromodeoxyuridine
additional information
-
inhibitory effects between pyrimidines and analogues
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
ATP is not necessary for the enzyme's catalytic function
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
adenosine deaminase deficiency
[Molecular pathology of immunological deficiency. Apropos of adenosine deaminase deficiency and nucleoside phosphorylase deficiency]
amidase deficiency
[Molecular pathology of immunological deficiency. Apropos of adenosine deaminase deficiency and nucleoside phosphorylase deficiency]
Anemia
Anergy, zinc deficiency, and decreased nucleoside phosphorylase activity in patients with sickle cell anemia.
Anemia, Hemolytic, Autoimmune
A patient with nucleoside phosphorylase deficiency, selective t-cell deficiency, and autoimmune hemolytic anemia.
Anemia, Hemolytic, Autoimmune
Primary immunodeficiencies (PIDs) presenting with cytopenias.
Anemia, Sickle Cell
Anergy, zinc deficiency, and decreased nucleoside phosphorylase activity in patients with sickle cell anemia.
Ataxia Telangiectasia
Normal activity of nucleoside phosphorylase, superoxide dismutase and catalase in skin fibroblasts cultured from ataxia-telangiectasia patients.
Common Variable Immunodeficiency
Common variable immunodeficiency and purine nucleotidase and nucleoside phosphorylase deficiency. A case report.
Down Syndrome
Erythrocyte adenosine deaminase, purine nucleoside phosphorylase and phosphoribosyltransferase activity in patients with Down's syndrome.
Down Syndrome
Levels of some purine metabolizing enzymes in lymphocytes from patients with Down's syndrome.
Liver Neoplasms, Experimental
Specificity of pyrimidine nucleoside phosphorylases and the phosphorolysis of 5-fluoro-2'-deoxyuridine.
Melanoma
Nucleotide-metabolism and chromosome alterations in human-malignant melanoma xenografts.
Neoplasms
Monoclonal antibody and enzymatic profiles of human malignant T-lymphoid cells and derived cell lines.
Neoplasms
Nucleoside-Catabolizing Enzymes in Mycoplasma-Infected Tumor Cell Cultures Compromise the Cytostatic Activity of the Anticancer Drug Gemcitabine.
Neoplasms
The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation.
purine-nucleoside phosphorylase deficiency
Mechanisms of deoxyguanosine lymphotoxicity. Human thymocytes, but not peripheral blood lymphocytes accumulate deoxy-GTP in conditions simulating purine nucleoside phosphorylase deficiency.
purine-nucleoside phosphorylase deficiency
On the metabolism of allopurinol. Formation of allopurinol-1-riboside in purine nucleoside phosphorylase deficiency.
purine-nucleoside phosphorylase deficiency
The metabolism of deoxyguanosine and guanosine in human B and T lymphoblasts. A role for deoxyguanosine kinase activity in the selective T-cell defect associated with purine nucleoside phosphorylase deficiency.
pyrimidine-nucleoside phosphorylase deficiency
A new form of nucleoside phosphorylase deficiency in two brothers with defective T-cell function.
pyrimidine-nucleoside phosphorylase deficiency
A patient with nucleoside phosphorylase deficiency, selective t-cell deficiency, and autoimmune hemolytic anemia.
pyrimidine-nucleoside phosphorylase deficiency
Another family with purine neucleoside phosphorylase deficiency.
pyrimidine-nucleoside phosphorylase deficiency
B cell hyperactivity and abnormalities in T cell markers and immunoregulatory function in a patient with nucleoside phosphorylase deficiency.
pyrimidine-nucleoside phosphorylase deficiency
Cellular immunodeficiency associated with nucleoside phosphorylase deficiency. Immunologic and biochemical studies.
pyrimidine-nucleoside phosphorylase deficiency
Common variable immunodeficiency and purine nucleotidase and nucleoside phosphorylase deficiency. A case report.
pyrimidine-nucleoside phosphorylase deficiency
Demonstration of Epstein-Barr virus in immunoblastic sarcoma of B-cells arising in a child with primary immunodeficiency disease.
pyrimidine-nucleoside phosphorylase deficiency
Immunotherapy and immunopathologic studies in a patient with nucleoside phosphorylase deficiency.
pyrimidine-nucleoside phosphorylase deficiency
Mechanisms of deoxyguanosine lymphotoxicity. Human thymocytes, but not peripheral blood lymphocytes accumulate deoxy-GTP in conditions simulating purine nucleoside phosphorylase deficiency.
pyrimidine-nucleoside phosphorylase deficiency
On the metabolism of allopurinol. Formation of allopurinol-1-riboside in purine nucleoside phosphorylase deficiency.
pyrimidine-nucleoside phosphorylase deficiency
Primary immunodeficiencies (PIDs) presenting with cytopenias.
pyrimidine-nucleoside phosphorylase deficiency
The metabolism of deoxyguanosine and guanosine in human B and T lymphoblasts. A role for deoxyguanosine kinase activity in the selective T-cell defect associated with purine nucleoside phosphorylase deficiency.
pyrimidine-nucleoside phosphorylase deficiency
[Molecular pathology of immunological deficiency. Apropos of adenosine deaminase deficiency and nucleoside phosphorylase deficiency]
Reperfusion Injury
Difference in onset of warm ischemia and reperfusion injury between parenchymal and endothelial cells of the liver. Evaluation by purine nucleoside phosphorylase and hyaluronic acid.
Sarcoma
Sheep gene mapping: additional DNA markers included (CASB, CASK, LALBA, IGF-1 and AMH).
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.158
uridine
wild-type, pH 7.5, temperature not specified in the publication
0.171
uridine
mutant H169A, pH 7.5, temperature not specified in the publication
additional information
additional information
-
Michaelis-Menten kinetics
-
additional information
additional information
Michaelis-Menten kinetics
-
additional information
additional information
-
Michaelis-Menten kinetics
-
additional information
additional information
Michaelis-Menten kinetics
-
additional information
additional information
Michaelis-Menten kinetics
-
additional information
additional information
Michaelis-Menten kinetics
-
additional information
additional information
linear regression analysis of the Michaelis-Menten and Lineweaver-Burk plots
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.7
uridine
mutant H169A, pH 7.5, temperature not specified in the publication
15
uridine
wild-type, pH 7.5, temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.113
3,5-bis-(4-chlorobenzoyl)-alpha-D-ribose 1-phosphate
Mycoplasma hyorhinis
-
substrate deoxythymidine, pH 7.6, 37°C
0.128
3,5-bis-(4-chlorobenzoyl)-alpha-D-ribose 1-phosphate
Mycoplasma hyorhinis
-
substrate 5-fluorodeoxyuridine, pH 7.6, 37°C
0.159
3,5-bis-(4-chlorobenzoyl)-alpha-D-ribose 1-phosphate
Mycoplasma hyorhinis
-
substrate 5-iododeoxyuridine pH 7.6, 37°C
0.188
3,5-bis-(4-chlorobenzoyl)-alpha-D-ribose 1-phosphate
Mycoplasma hyorhinis
-
substrate uridine, pH 7.6, 37°C
0.5
5-chloro-6-(1-[2-iminopyrrolidinyl]methyl)uracil
Mycoplasma hyorhinis
-
substrate deoxythymidine, pH 7.6, 37°C
0.5
5-chloro-6-(1-[2-iminopyrrolidinyl]methyl)uracil
Mycoplasma hyorhinis
-
substrate uridine, pH 7.6, 37°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.46
purified recombinant His-tagged enzyme, pH 7.0, 25°C
11.2
substrate deoxyuridine, pH 7.5, temperature not specified in the publication
28.4
purified recombinant enzyme, pH 8.0, 50°C, substrate uridine
37.5
purified recombinant enzyme, pH 8.0, 50°C, substrate uridine
43.3
purified recombinant enzyme, pH 8.5, 50°C, substrate uridine
5.9
substrate thymidine, pH 7.5, temperature not specified in the publication
8.1
substrate uridine, pH 7.5, temperature not specified in the publication
98.3
purified recombinnat enzyme, pH 8.5, 50°C, substrate uridine
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 6
6.9
7 - 11.5
7.5
8.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 10.5
activity range, profile overview, recombinant enzyme
6 - 12
-
pH 6.0: about 75% of maximal activity, pH 12.0: about 80% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
50
60
70
99
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40 - 70
activity range, profile overview, recombinant enzyme
additional information
additional information
thermophilic signature of the enzyme, overview
additional information
thermophilic signature of the enzyme, overview
additional information
thermophilic signature of the enzyme, overview
additional information
thermophilic signature of the enzyme, overview
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
PyNPase level quantified by sandwich ELISA using monoclonal anti-human thimidine phosphorylase antibodies 104B and 232-2, no association between PyNPase level and recurrence, disease-free survival at year 2.2 better with low PyNPase levels and high PyNPase-to-dihydropyrimidine dihydrogenase ratio
brenda
-
PyNPase level quantified by sandwich ELISA using monoclonal anti-human thimidine phosphorylase antibodies 104B and 232-2
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
inhibitors, such as 5-benzylacyclouridine (BAU), block the activity of uridine phosphorylase, inducing an increase in the plasma concentrations of uridine. This phenomenon, designated as uridine rescue, benefits the chemotherapeutic effect of 5-fluorouracil on colon cancer
metabolism
uridine phosphorylase is a critical enzyme in pyrimidine salvage metabolism
physiological function
the enzyme catalyzes reversible phosphorolysis of uridine to uracil and ribose-1-phosphate, and is responsible for maintenance of the uridine concentration in cells. Uridine phosphorylase is ubiquitously expressed in all living organisms, from bacteria to human, supporting an important role in cell survivability
additional information
evolution
pyrimidine-nucleoside phosphorylase is a member of the NP-II family, implying that it has a two-domain structure and functions as a dimer
evolution
the enzyme belongs to the NP family II
additional information
analysis of the three-dimensional structures of the nucleoside-binding sites in subunits A and B of BsPyNP complexed with imidazole. The imidazole (IMD) molecule is localized in the active site of both subunits. IMD interacts with the enzyme residues via hydrogen bonds and a stacking interaction
additional information
-
analysis of the three-dimensional structures of the nucleoside-binding sites in subunits A and B of BsPyNP complexed with imidazole. The imidazole (IMD) molecule is localized in the active site of both subunits. IMD interacts with the enzyme residues via hydrogen bonds and a stacking interaction
additional information
dynamic modelling of phosphorolytic cleavage catalyzed by pyrimidine-nucleoside phosphorylase, differential-dynamical model, kinetics, overview. Py-NPase-catalyzed phosphorylic cleavage reactions are reversible reactions proceeding towards a dynamic equilibrium. The reaction trajectory until equilibrium does not only depend on physical parameters, like temperature and pressure, but also on enzyme concentration, the concentration of substrates, or the presence of products
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
homohexamer
6 * 27000, the functional unit is a hexamer with alpha/beta-fold configuration
?
x * 46000, SDS-PAGE, x * 46271, calculated from sequence
dimer
revealed by dynamic light-scattering (DynaPro MS/X) of the purified protein, 20 mg protein/ml, 18°C, 20 mM Tris-HCl pH 7.6, 200 mM sodium chloride, particle size distribution with a polydispersity of 18.7%
dimer
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
revealed by dynamic light-scattering (DynaPro MS/X) of the purified protein, 20 mg protein/ml, 18°C, 20 mM Tris-HCl pH 7.6, 200 mM sodium chloride, particle size distribution with a polydispersity of 18.7%
-
homodimer
the enzyme has a two-domain structure and functions as a dimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme in complex with imidazole and sulfate, sitting drop vapour diffusion, mixing of 0.002 ml of 16 mg/ml protein in 20 mM Tris-HCl, 500 mM KCl with 0.002 ml of reservoir solution containing 0.2 M ammonium acetate, 0.1 M bis-Tris, pH 5.5, X-ray diffraction structure determination and analysis at 1.88 A resolution
crystal structure of the enzyme with the substrate analog, pseudouridine, in its active site is solved to 2.1 A
-
hanging-drop vapor diffusion method, crystals of the protein-inhibitor complex with the substrate analog pseudouridine
-
in complex with the products, ribose 1-phosphate and uracil, at 1.8 A resolution. The biological unit is a hexamer with an alpha/beta monomeric fold. Residue His169 structurally aligns with Arg168 of the Escherichia coli uridine phosphorylase structure. A second active site residue, Lys162, is not present in previously determined uridine phosphorylase structures and interacts with O2 of uracil
crystallized at 18°C using the oil-microbatch method with PEG 4000 as a precipitant. A native data set is collected to 1.8 A resolution using synchrotron radiation. The crystal belongs to the monoclinic space group P2(1), with unit-cell parameters a = 58.83, b = 76.23, c = 103.86 A, beta = 91.3
crystals: monoclinic with dimensions of 0.13 * 0.13 * 0.07 mm, X-ray diffraction to 1.8 Å using synchrotron radiation at -173°C, belong to space group P2(1), asymmetric unit contains dimer with local pseudo-twofold symmetry, unit-cell parameters: a: 58.83, b: 76.23, c: 103.86, beta: 91.3°, oil-microbatch method: 1 week at 18°C, drop: 0.5 microlitre precipitant solution (27.5% (w/v) PEG 4000 in 100 mM HEPES-NaOH pH 7.5, 10 mM CaCl2) + 0.5 microlitre protein solution (21.7 mg/ml in 20 mM Tris-HCl pH8, 200 NaCl)
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40
purified recombinant enzyme, pH 8.5, 1 h, 90% activity remaining
45
purified recombinant enzyme, pH 8.5, 1 h, 80% activity remaining
50
55
purified recombinant enzyme, pH 8.5, 1 h, 70% activity remaining
60
70
80
50
purified recombinant enzyme, pH 8.5, 1 h, 65.6% activity remaining
50
purified recombinant enzyme, pH 8.5, 1 h, 75% activity remaining
50
purified recombinant enzyme, pH 8.5, 1 h, 43.7% activity remaining
50
purified recombinant enzyme, pH 8.5, 1 h, 52.1% activity remaining
60
purified recombinant enzyme, pH 8.5, 1 h, 10% activity remaining
70
-
half-life: 25 min in 20 mM potassium phosphate, 15.1 h in 20 mM potassium phosphate and 1 mM 5-methyluridine
70
purified enzyme, half-life is 23 min in the presence of 20 mM potassium phosphate and 1 mM inosine, and 15.1 h in the presence of 20 mM potassium phosphate and 1 mM 5-methyluridine
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
Escherichia coli uridine phosphorylase is destabilized in the presence of ATP. ATP alters protein folding and function of the enzyme. ATP specifically accelerates the unfolding rate of uridine phosphorylase with no observable effects on the refolding process, ATP binding mechanism analysis. Purified UPase remains folded following treatment with 0 to about 4 M urea, and unfolding occurred from 4 to 6 M urea in the absence of ATP. Partially unfolded intermediate states of UPase accumulate in the presence of ATP. ATP interacts with a transition state close to the folded state.
repeated cycles of freezing and thawing inactivate the enzyme if phosphate is absent
-
the enzyme is quite labile during the course of purification, dithiothreitol and glycerol are required for stability
-
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the purified enzyme is stable at 50% DMF, 50% DMSO, and 50% 2-MeTHF
758850
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, in presence of phosphate, glycerol and dithiothreitol, stable for 6 months
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
harvested with 5 mM 2-mercaptoethanol and 500 mM NaCl in Tris-HCl pH 8, extract desalted with HiPrep 2610, recombinant protein eluted with 0-300 mM NaCl from Super Q Toyopearl 650M column, eluted from Bio-Scale CHT-20-1 column with 10-100 mM NaCl in phosphate-NaOH pH 7, concentrated by ultracentrifugation with 10 kDa cut-off, eluted from HiLoad 16/60 Superdex 200 prep-grade column with 200 mM NaCl in Tris-HCl pH 8, concentrated by ultracentrifugation to 21.7 mg/ml, stored at -70 °C
recombinant enzyme from Escherichia coli strain BL21(DE3) by dialysis, anion exchange chromatography, and gel filtration
recombinant N-terminally His6-tagged Py-NPase from Escherichia coli strain BL21 by nickel affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression of enzymes with uridine and thymidine phosphorylase activities in strain BL21(DE3)
-
gene mining using the sequence of Geobacillus stearothermophilus gene pdp (UniProt ID P77836) as search model, recombinant expression in Escherichia coli strain BL21(DE3), sequence comparisons
gene udp, recombinant expression in Escherichia coli strain BL21(DE3)
recombinant expression of N-terminally His6-tagged Py-NPase in Escherichia coli strain BL21
gene mining using the sequence of Geobacillus stearothermophilus gene pdp (UniProt ID P77836) as search model, recombinant expression in Escherichia coli strain BL21(DE3), sequence comparisons
-
gene mining using the sequence of Geobacillus stearothermophilus gene pdp (UniProt ID P77836) as search model, recombinant expression in Escherichia coli strain BL21(DE3), sequence comparisons
gene mining using the sequence of Geobacillus stearothermophilus gene pdp (UniProt ID P77836) as search model, recombinant expression in Escherichia coli strain BL21(DE3), sequence comparisons
gene mining using the sequence of Geobacillus stearothermophilus gene pdp (UniProt ID P77836) as search model, recombinant expression in Escherichia coli strain BL21(DE3), sequence comparisons
gene mining using the sequence of Geobacillus stearothermophilus gene pdp (UniProt ID P77836) as search model, recombinant expression in Escherichia coli strain BL21(DE3), sequence comparisons
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
presence of 5-15 mM cytidine or CMP distinctly increases the activities of purine nucleoside phosphorylase, uridine phosphorylase and thymidine phosphorylase when added into medium from 0 to 8 h
-
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme, unfolding equilibrium of UPase in 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 5.0 mM MgCl2, 1.0 mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP), and 10 M urea at pH 8.0, 25°C overnight. Monitoring by pulse proteolysis. Cm values are measured by fitting the band intensities on SDS-PAGE with varying urea concentrations to a simple two-state model. Data are fitted to the two-state model in the absence of ATP and to a three-state model in the presence of ATP. Purified UPase remains folded following treatment with 0 to about 4 M urea, and unfolding occurs from 4 to 6 M urea in the absence of ATP. For refolding experiments, 0.4 mg/ml UPase are initially incubated overnight in 20 mM Tris-HCl buffer, pH 8.0, containing 50 mM NaCl, 5.0 mM MgCl2, 1.0 mM TCEP, and 7.5 M urea to induce the unfolded state. Refolding is then performed by diluting samples five times into refolding buffer to reach the following final conditions: 0.08 mg/ml UPase, 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 5.0 MgCl2, 1.0 mM TCEP, and 1.5 M urea with or without 2.0 mM ATP. Partially unfolded intermediate states of UPase accumulate in the presence of ATP
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
-
the cytostatic and antiviral activity of pyrimidine nucleoside analogues is markedly decreased by a Mycoplasma hyorhinis infection and the phosphorolytic activity of the mycoplasmas is responsible for this
synthesis
synthesis
-
overexpression of enzyme in Escherichia coli, medium optimization and presence of uridine and 5-fluorouracil results in conversion of more than 90% of uridine to 5-fluorouridine by the cells
synthesis
the enzyme is useful in biocatalytic production of 2,6-dichloropurine 2'-deoxyriboside and 6-chloro-2-fluoropurine 2'-deoxyriboside
synthesis
the enzyme is useful in biocatalytic production of 2-chloro-2'-deoxyadenosine (cladribine), adenine-arabinoside, 2-fluoroadenine arabinoside, and 5-methyluridine
synthesis
the enzyme is useful in biocatalytic production of 2-chloroadenine riboside, 2-fluoroadenine riboside, 2,6-diaminopurine 2'-deoxyriboside, 2-chloro-2'-deoxyadenosine, 2-fluoro-2'-deoxyadenosine, 2'-deoxy-2'-fluoroadenosine, 2'-deoxy-2'-fluoro-arabinofuranosyl adenine, 2,6-diaminopurine arabinoside, 2,6-dichloropurine arabinoside, 6-chloro-2-fluoropurine arabinoside, and 5-iododeoxyuridine
synthesis
-
during enzymatic synthesis of adenine arabinoside from adenine and uracil arabinoside with wet cells of Klebsiella aerogenes induced by cytidine or CMP, the reaction time can be shortened from 36 to 6 h
synthesis
-
overexpression of enzyme in Escherichia coli, medium optimization and presence of uridine and 5-fluorouracil results in conversion of more than 90% of uridine to 5-fluorouridine by the cells
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hamamoto, T.; Noguchi, T.; Midorikawa, Y.
Purification and characterization of purine nucleoside phosphorylase and pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus TH 6-2
Biosci. Biotechnol. Biochem.
60
1179-1180
1996
Haemophilus influenzae, Haemophilus influenzae TH 6-2
brenda
Scocca, J.J.
Purification and substrate specificity of pyrimidine nucleoside phosphorylase from Haemophilus influenzae
J. Biol. Chem.
246
6606-6610
1971
Haemophilus influenzae
brenda
Saunders, P.P.; Wilson, B.A.; Saunders, G.F.
Purification and comparative properties of a pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus
J. Biol. Chem.
244
3691-3697
1969
Geobacillus stearothermophilus
brenda
Pugmire, M.J.; Ealick, S.E.
The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation
Structure
6
1467-1479
1998
Geobacillus stearothermophilus
brenda
Zhou, M.; Pugmire, M.J.; Vuong, B.Q.; Ealick, S.E.
Cloning, expression and crystallization of pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus
Acta Crystallogr. Sect. D
55
287-290
1999
Geobacillus stearothermophilus
brenda
Scocca, J.J.
Pyrimidine nucleoside phosphorylase from Haemophilus influenzae
Methods Enzymol.
51
432-437
1978
Haemophilus influenzae
brenda
Hori, N.; Watanabe, M.; Yamazaki, Y.; Mikami, Y.
Purification and characterization of thermostable pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus
Agric. Biol. Chem.
54
763-768
1990
Geobacillus stearothermophilus, Geobacillus stearothermophilus JTS 859
-
brenda
Zaks, A.; Dodds, D.R.
Application of biocatalysts and biotransformation to the synthesis of pharmaceuticals
Drug Discov. Today
2
513-531
1997
Pectobacterium carotovorum
-
brenda
Panova, N.G.; Shcheveleva, E.V.; Alexeev, C.S.; Mukhortov, V.G.; Zuev, A.N.; Mikhailov, S.N.; Esipov, R.S.; Chuvikovsky, D.V.; Miroshnikov, A.I.
Use of 4-thiouridine and 4-thiothymidine in studies on pyrimidine nucleoside phosphorylases
Mol. Biol.
38
770-776
2004
Escherichia coli
-
brenda
Shimizu, K.; Kunishima, N.
Purification, crystallization and preliminary X-ray diffraction study on pyrimidine nucleoside phosphorylase TTHA1771 from Thermus thermophilus HB8
Acta Crystallogr. Sect. F
63
308-310
2007
Thermus thermophilus, Thermus thermophilus (Q5SHF9), Thermus thermophilus HB8 / ATCC 27634 / DSM 579, Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q5SHF9)
brenda
Gao, X.F.; Huang, X.R.; Sun, C.C.
Role of each residue in catalysis in the active site of pyrimidine nucleoside phosphorylase from Bacillus subtilis: a hybrid QM/MM study
J. Struct. Biol.
154
20-26
2006
Bacillus subtilis (P39142), Bacillus subtilis
brenda
Nishioka, M.; Miyamoto, H.; Kurita, N.; Higashijima, J.; Yoshikawa, K.; Miyatani, T.; Shimada, M.
Pyrimidine nucleoside phosphorylase and dihydropyrimidine dihydrogenase activities as predictive factors for the efficacy of doxifluridine together with mitomycin C as adjuvant chemotherapy in primary colorectal cancer
Hepatogastroenterology
54
1089-1093
2007
Homo sapiens
brenda
Tang, Y.; Ni, M.; Wu, W.; Sun, J.; Zhou, C.
Biotransformation of the antitumor intermediate 5-fluorouridine by recombinant Escherichia coli with high pyrimidine nucleoside phosphorylase activity
Biocatal. Biotransform.
28
130-136
2010
Klebsiella aerogenes, Klebsiella aerogenes CMCC 45103
-
brenda
Vande Voorde, J.; Gago, F.; Vrancken, K.; Liekens, S.; Balzarini, J.
Characterization of pyrimidine nucleoside phosphorylase of Mycoplasma hyorhinis: implications for the clinical efficacy of nucleoside analogues
Biochem. J.
445
113-123
2012
Mycoplasma hyorhinis
brenda
Vande Voorde, J.; Quintiliani, M.; McGuigan, C.; Liekens, S.; Balzarini, J.
Inhibition of pyrimidine and purine nucleoside phosphorylases by a 3,5-dichlorobenzoyl-substituted 2-deoxy-D-ribose-1-phosphate derivative
Biochem. Pharmacol.
83
1358-1363
2012
Mycoplasma hyorhinis
brenda
Tran, T.H.; Christoffersen, S.; Allan, P.W.; Parker, W.B.; Piskur, J.; Serra, I.; Terreni, M.; Ealick, S.E.
The crystal structure of Streptococcus pyogenes uridine phosphorylase reveals a distinct subfamily of nucleoside phosphorylases
Biochemistry
50
6549-6558
2011
Streptococcus pyogenes (Q5XA29), Streptococcus pyogenes
brenda
Szeker, K.; Zhou, X.; Schwab, T.; Casanueva, A.; Cowan, D.; Mikhailopulo, I.; Neubauer, P.
Comparative investigations on thermostable pyrimidine nucleoside phosphorylases from Geobacillus thermoglucosidasius and Thermus thermophilus
J. Mol. Catal. B
84
27-34
2012
Parageobacillus thermoglucosidasius, Thermus thermophilus (Q72HS4), Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 (Q72HS4)
-
brenda
Serra, I.; Bavaro, T.; Cecchini, D.; Daly, S.; Albertini, A.; Terreni, M.; Ubiali, D.
A comparison between immobilized pyrimidine nucleoside phosphorylase from Bacillus subtilis and thymidine phosphorylase from Escherichia coli in the synthesis of 5-substituted pyrimidine 2'-deoxyribonucleosides
J. Mol. Catal. B
95
16-22
2013
Bacillus subtilis
-
brenda
Vande Voorde, J.; Liekens, S.; Gago, F.; Balzarini, J.
The pyrimidine nucleoside phosphorylase of Mycoplasma hyorhinis and how it may affect nucleoside-based therapy
Nucleosides Nucleotides Nucleic Acids
33
394-402
2014
Mycoplasma hyorhinis, Mycoplasma hyorhinis ATCC 17981
brenda
Balaev, V.V.; Prokofev, I.I.; Gabdoulkhakov, A.G.; Betzel, C.; Lashkov, A.A.
Crystal structure of pyrimidine-nucleoside phosphorylase from Bacillus subtilis in complex with imidazole and sulfate
Acta Crystallogr. Sect. F
74
193-197
2018
Bacillus subtilis (P39142), Bacillus subtilis
brenda
Liu, Y.K.; Lin, T.H.; Liu, P.F.
ATP alters protein folding and function of Escherichia coli uridine phosphorylase
Arch. Biochem. Biophys.
634
11-20
2017
Escherichia coli (P0C037)
brenda
Kamel, S.; Thiele, I.; Neubauer, P.; Wagner, A.
Thermophilic nucleoside phosphorylases their properties, characteristics and applications
Biochim. Biophys. Acta
1868
140304
2020
Parageobacillus thermoglucosidasius (A0A178U4P5), Bacillus subtilis (P39142), Geobacillus stearothermophilus (P77836), Thermus thermophilus (Q72HS4), Bacillus subtilis 168 (P39142)
brenda
Liu, K.; Zhou, Y.; Zhang, J.; Chu, J.; Zhang, Y.; He, B.
A thermostable pyrimidine nucleoside phosphorylase from Brevibacillus borstelensis LK01 for synthesizing halogenated nucleosides
Biotechnol. Lett.
39
1903-1910
2017
Siminovitchia fordii, Serratia marcescens (A0A080UUN2), Aneurinibacillus migulanus (A0A0D1XZI7), Lacticaseibacillus paracasei (A0A0E2M090), Brevibacillus borstelensis (A0A1S5VH74), Brevibacillus borstelensis, Serratia marcescens MH6 (A0A080UUN2), Brevibacillus borstelensis LK01 (A0A1S5VH74), Aneurinibacillus migulanus U603 (A0A0D1XZI7)
brenda
Alexeev, C.S.; Sivets, G.G.; Safonova, T.N.; Mikhailov, S.N.
Substrate specificity of E. coli uridine phosphorylase. Further evidences of high-syn conformation of the substrate in uridine phosphorolysis
Nucleosides Nucleotides Nucleic Acids
36
107-121
2017
Escherichia coli (P0C037)
brenda
Giessmann, R.; Krausch, N.; Kaspar, F.; Bournazou, M.; Wagner, A.; Neubauer, P.; Gimpel, M.
Dynamic modelling of phosphorolytic cleavage catalyzed by pyrimidine-nucleoside phosphorylase
Processes
7
380
2019
Parageobacillus thermoglucosidasius (A0A178U4P5)
-
brenda
Okuyama, K.; Hamamoto, T.; Noguchi, T.; Midorikawa, Y.
Molecular cloning and expression of the pyrimidine nucleoside phosphorylase gene from Bacillus stearothermophilus TH 6-2
Biosci. Biotechnol. Biochem.
60
1655-1659
1996
Geobacillus stearothermophilus (P77836), Geobacillus stearothermophilus
brenda
Wei, X.K.; Ding, Q.B.; Zhang, L.; Guo, Y.L.; Ou, L.; Wang, C.L.
Induction of nucleoside phosphorylase in Enterobacter aerogenes and enzymatic synthesis of adenine arabinoside
J. Zhejiang Univ. Sci. B
9
520-526
2008
Klebsiella aerogenes
brenda
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