Information on EC 2.4.2.2 - pyrimidine-nucleoside phosphorylase

New: Word Map on EC 2.4.2.2
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Mark a special word or phrase in this record:
Search Reference ID:
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
2.4.2.2
-
RECOMMENDED NAME
GeneOntology No.
pyrimidine-nucleoside phosphorylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2'-deoxyuridine + phosphate = uracil + 2-deoxy-alpha-D-ribose 1-phosphate
show the reaction diagram
molecular basis of catalytic chamber-assisted unfolding and cleavage of human insulin by human insulin-degrading enzyme, IDE utilizes the interaction of its exosite with the N-terminus of the insulin A chain, overview. The unique size, shape, charge distribution, and exosite of the IDE catalytic chamber contribute to its high affinity for insulin
-
-
-
thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate
show the reaction diagram
(2)
-
-
-
uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
show the reaction diagram
; (1)
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pentosyl group transfer
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Metabolic pathways
-
-
nucleoside and nucleotide degradation (archaea)
-
-
pyrimidine deoxyribonucleosides degradation
-
-
Pyrimidine metabolism
-
-
pyrimidine ribonucleosides degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
pyrimidine-nucleoside:phosphate 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 ribonucleoside uridine and the 2'-deoxyribonucleosides 2'-deoxyuridine and thymidine [3]. 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.
CAS REGISTRY NUMBER
COMMENTARY hide
9055-35-0
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
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
show the reaction diagram
-
1.6% substrate conversion after 30 min
-
?
1,2,4-triazole-3-carboxamide + alpha-D-ribose 1-phosphate
ribavirin + phosphate
show the reaction diagram
-
-
-
-
-
2'-deoxy-2'-fluorouridine + phosphate
?
show the reaction diagram
-
-
poor activity, 0.4% substrate conversion after 30 min
-
?
2'-deoxy-2'-fluorouridine + phosphate
uracil + 2-deoxy-2-fluoro-alpha-D-ribose 1-phosphate
show the reaction diagram
-
15.6% substrate conversion after 30 min
-
?
4-thiothymidine + phosphate
4-thiothymin + alpha-D-ribose 1-phosphate
show the reaction diagram
-
uridine phosphorylase activity, see also EC 2.4.2.3
-
-
r
4-thiouridine + phosphate
4-thiouracil + alpha-D-ribose 1-phosphate
show the reaction diagram
-
thymidine phosphorylase activity, see also EC 2.4.2.4
-
-
r
5'-deoxy-5-fluorouridine + phosphate
5-fluorouracil + alpha-D-deoxyribose 1-phosphate
show the reaction diagram
-
-
5-fluorouracil is a chemotherapeutic agent and inactivated by dihydropyrimidine dihydrogenase activity
-
?
5-bromodeoxyuridine + phosphate
5-bromouracil + 2-deoxy-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
5-bromodeoxyuridine + phosphate
5-bromouracil + deoxyribose 1-phosphate
show the reaction diagram
5-bromouridine + phosphate
5-bromouracil + alpha-D-ribose 1-phosphate
show the reaction diagram
5-chlorodeoxyuridine + phosphate
5-chlorouracil + 2-deoxy-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
5-fluorodeoxyuridine + phosphate
5-fluorouracil + 2-deoxy-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
5-fluorouridine + phosphate
5-fluorouracil + alpha-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
5-iododeoxyuridine + phosphate
5-iodouracil + 2-deoxy-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
5-iodouridine + phosphate
5-iodouracil + alpha-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
show the reaction diagram
5-trifluoromethyl-2'-deoxyuridine + phosphate
5-trifluoromethyluracil + 2-deoxy-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
cytidine + phosphate
cytosine + alpha-D-ribose 1-phosphate
show the reaction diagram
deoxyuridine + phosphate
uracil + 2-deoxy-D-ribose 1-phosphate
show the reaction diagram
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
show the reaction diagram
ribofuranosyl thymine + phosphate
thymine + alpha-D-ribose 1-phosphate
show the reaction diagram
thymidine + phosphate
thymine + 2-deoxy-D-ribose 1-phosphate
show the reaction diagram
thymidine + phosphate
thymine + alpha-D-deoxyribose 1-phosphate
show the reaction diagram
-
-
-
r
uracil arabinoside + phosphate
uracil + alpha-D-arabinose 1-phosphate
show the reaction diagram
-
-
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
show the reaction diagram
additional information
?
-
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3,5-bis-(4-chlorobenzoyl)-alpha-D-ribose 1-phosphate
-
competitive inhibition with regard to inosine
5-benzylacyclouridine
-
-
5-chloro-6-(1-[2-iminopyrrolidinyl]methyl)uracil
-
-
7-deazaxanthine
-
-
uridine
-
above 15 mM, competitive inhibition of cleavage of 5-bromodeoxyuridine
additional information
-
inhibitory effects between pyrimidines and analogues
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.58
2'-deoxyuridine
-
-
0.25
4-thiothymidine
-
pH 7.5, 25C, thymidine phosphorylase activity
0.13
4-thiouridine
-
pH 7.5, 25C, uridine phosphorylase activity
0.1
5-bromodeoxyuridine
-
-
0.03
5-Bromouridine
-
-
0.169
5-fluorodeoxyuridine
-
pH 7.6, 37C
0.047
5-fluorouridine
-
pH 7.6, 37C
0.144
5-iododeoxyuridine
-
pH 7.6, 37C
0.069
5-iodouridine
-
pH 7.6, 37C
0.07 - 0.32
5-methyluridine
0.13 - 0.578
deoxyuridine
0.38 - 0.797
phosphate
0.11 - 1.9
thymidine
0.092 - 2.3
uridine
additional information
additional information
-
kinetics
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
63
4-thiothymidine
Escherichia coli
-
pH 7.5, 25C, thymidine phosphorylase activity
49
4-thiouridine
Escherichia coli
-
pH 7.5, 25C, uridine phosphorylase activity
11.9
5-fluorodeoxyuridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
6.1
5-fluorouridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
9.5
5-iododeoxyuridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
6.4
5-iodouridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
24.6
deoxyuridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
8.6 - 17.5
phosphate
21.6 - 679
thymidine
1.7 - 277
uridine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
70
5-fluorodeoxyuridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
3977
130
5-fluorouridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
2938
66
5-iododeoxyuridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
8023
93
5-iodouridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
7447
43
deoxyuridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
1060
22
phosphate
Mycoplasma hyorhinis
-
cosubstrate deoxythymidine, pH 7.6, 37C; cosubstrate uridine, pH 7.6, 37C
16
46
thymidine
Mycoplasma hyorhinis
-
pH 7.6, 37C
166
92
uridine
Mycoplasma hyorhinis
-
pH 7.6, 37C
261
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25
uridine
-
-
additional information
additional information
-
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.113 - 0.188
3,5-bis-(4-chlorobenzoyl)-alpha-D-ribose 1-phosphate
0.000003 - 0.000005
5-benzylacyclouridine
0.5
5-chloro-6-(1-[2-iminopyrrolidinyl]methyl)uracil
Mycoplasma hyorhinis
-
substrate deoxythymidine, pH 7.6, 37C; substrate uridine, pH 7.6, 37C
0.03 - 0.06
7-deazaxanthine
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
11.2
substrate deoxyuridine, pH 7.5, temperature not specified in the publication
45
-
purified recombinant enzyme
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2
-
uridine, thymidine
7.4
-
ribonucleosides and uracil arabinoside
7.5
-
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 12
-
pH 6.0: about 75% of maximal activity, pH 12.0: about 80% of maximal activity
6.9 - 7.4
-
pH 6.9: optimum, pH 7.4: 75% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
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
Manually annotated by BRENDA team
-
PyNPase level quantified by sandwich ELISA using monoclonal anti-human thimidine phosphorylase antibodies 104B and 232-2
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Staphylococcus aureus (strain COL)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45400
estimated according to amino acid composition
78000
-
sedimentation velocity analysis
85000
-
gel filtration
86300
in the dimeric state of the purified protein
92000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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 18C 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 using synchrotron radiation at -173C, 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 18C, 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)
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
-
stable
489698
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80
-
1 h, 20 mM potassium phosphate, complete inactivation
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, in presence of phosphate, glycerol and dithiothreitol, stable for 6 months
-
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 enzymes
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression of enzymes with uridine and thymidine phosphorylase activities in strain BL21(DE3)
-
pET-11a for expression in Escherichia coli BL21 (DE3)
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H169A
about 10% of wild-type activity
H169D
about 1% of wild-type activity
H169N
about 4% of wild-type activity
K162A
complete loss of activity
V220D
almost complete loss of activity
V220E
less than 0.5% of wild-type activity
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
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
Show AA Sequence (983 entries)
Please use the Sequence Search for a certain query.