Information on EC 2.4.2.3 - uridine phosphorylase

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

EC NUMBER
COMMENTARY hide
2.4.2.3
-
RECOMMENDED NAME
GeneOntology No.
uridine phosphorylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pentosyl group transfer
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Drug metabolism - other enzymes
-
-
Metabolic pathways
-
-
nucleoside and nucleotide degradation (archaea)
-
-
pyrimidine deoxyribonucleosides degradation
-
-
pyrimidine metabolism
-
-
Pyrimidine metabolism
-
-
pyrimidine ribonucleosides degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
uridine:phosphate alpha-D-ribosyltransferase
The enzyme participates the the pathways of pyrimidine ribonucleosides degradation and salvage. The mammalian enzyme also accepts 2'-deoxyuridine.
CAS REGISTRY NUMBER
COMMENTARY hide
9030-22-2
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
Aeropyrum pernix DSM 11879
-
SwissProt
Manually annotated by BRENDA team
cattle
-
-
Manually annotated by BRENDA team
AJ 11125
-
-
Manually annotated by BRENDA team
AJ 11125
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
tapeworm
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
wild type and uridine phosphorylase deficient strain
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2'-deoxyuridine + phosphate
uracil + deoxyribose 1-phosphate
show the reaction diagram
5'-deoxy-5-fluorouridine + alpha-D-ribose 1-phosphate
5'-deoxy-5-fluorouridine + phosphate
show the reaction diagram
-
-
-
-
?
5'-deoxy-5-fluorouridine + phosphate
5-fluorouracil + 5-deoxyribose-1-phosphate
show the reaction diagram
5-bromo-2'-deoxyuridine + phosphate
5-bromouracil + 2-deoxribose 1-phosphate
show the reaction diagram
5-bromouracil + deoxyribose 1-phosphate
5-bromodeoxyuridine + phosphate
show the reaction diagram
5-bromouridine + phosphate
5-bromouracil + alpha-D-ribose 1-phosphate
show the reaction diagram
5-fluoro-2'-deoxyuridine + phosphate
5-fluorouracil + 2-deoxy-alpha-D-ribose 1-phosphate
show the reaction diagram
-
-
-
?
5-fluoro-2'-deoxyuridine + phosphate
5-fluorouracil + 2-deoxy-D-ribose-1-phosphate
show the reaction diagram
-
-
also accepts 2'-deoxypyrimidine nucleosides in higher organisms
-
r
5-fluoro-2'-deoxyuridine + phosphate
5-fluorouracil + 2-deoxyribose-1-phosphate
show the reaction diagram
5-fluorouracil + alpha-D-ribose 1-phosphate
5-fluorouridine + phosphate
show the reaction diagram
-
-
-
-
?
5-fluorouracil + alpha-D-ribose-1-phosphate
5-fluorouridine + phosphate
show the reaction diagram
5-fluorouridine + phosphate
5-fluorouracil + alpha-D-ribose 1-phosphate
show the reaction diagram
5-fluorouridine + phosphate
5-fluorouracil + alpha-D-ribose-1-phosphate
show the reaction diagram
5-methyluridine + phosphate
5-methyluracil + alpha-D-ribose 1-phosphate
show the reaction diagram
5-methyluridine + phosphate
thymine + alpha-D-ribose 1-phosphate
show the reaction diagram
-
19% of the activity with uridine
-
-
?
arabinofuranosyl-5-ethyluracil + phosphate
5-ethyluracil + arabinose-1-phosphate
show the reaction diagram
-
weak substrate
-
-
?
azathymine + deoxyribose 1-phosphate
azadeoxythymidine + phosphate
show the reaction diagram
-
-
-
-
ir
azauracil + deoxyribose 1-phosphate
azadeoxyuridine + phosphate
show the reaction diagram
-
-
-
-
?
azauracil + ribose 1-phosphate
azauridine + phosphate
show the reaction diagram
-
-
-
-
ir
cytidine + phosphate
cytosine + alpha-D-ribose 1-phosphate
show the reaction diagram
-
-
-
-
?
deoxyuridine + phosphate
uracil + 2-deoxy-alpha-D-ribose 1-phosphate
show the reaction diagram
deoxyuridine + phosphate
uracil + deoxy-D-ribose 1-phosphate
show the reaction diagram
fluorouridine + phosphate
fluorouracil + alpha-D-ribose-1-phosphate
show the reaction diagram
guanosine + phosphate
guanine + alpha-D-ribose 1-phosphate
show the reaction diagram
10% of the activity with uridine
-
-
r
inosine + phosphate
hypoxanthine + alpha-D-ribose 1-phosphate
show the reaction diagram
-
-
-
?
pyrimidine nucleoside + phosphate
pyrimidine base + alpha-D-ribose 1-phosphate
show the reaction diagram
-
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
thymidine + phosphate
thymine + alpha-D-ribose 1-phosphate
show the reaction diagram
thymine + deoxyribose 1-phosphate
deoxythymidine + phosphate
show the reaction diagram
-
-
-
-
?
thymine + ribose 1-phosphate
thymidine + phosphate
show the reaction diagram
-
-
-
-
?
uracil + alpha-D-ribose 1-phosphate
uridine + phosphate
show the reaction diagram
uracil arabinoside + phosphate
uracil + arabinose-1-phosphate
show the reaction diagram
uridine + arsenate
?
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
-
most pyrimidine nucleosides except for 4-amino-substituted species like deoxycytidine
or alpha-D-deoxyribose 1-phosphate
-
r
uracil + alpha-D-ribose 1-phosphate
uridine + phosphate
show the reaction diagram
-
uridine prevents the glucose deprivation-induced death of immunostimulated astrocytes via the action of uridine phosphorylase
-
-
?
uridine + phosphate
uracil + alpha-D-ribose 1-phosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
stabilizes the enzyme, which possesses an intermolecular metal-binding site, structure, overview
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-((2-pyrrolidine-1-yl)ethyl)uracil
inhibits both enzymic activity and growth of Plasmodium falciparum
1-(1',2'-dihydroxypropyl)-5,6-tetramethyleneuracil
-
only the R-enantiomer inhibits, but not the S-enantiomer
1-(1',3'-dihydroxy-2'-propoxy)methyl-5,6-tetramethyleneuracil
-
inhibits forward and reverse reaction
1-(1',3'-dihydroxy-2'-propoxy)methyl-5-benzyluracil
-
i.e. DHPBU, competitive
2',3'-Dideoxy-5-ethyluridine
-
-
2'-deoxyglycosylthymine
-
-
2'-deoxylyxofuranosyl-5-ethyluracil
-
-
2,2'-Anhydro-5-ethyluridine
2,3'-Anhydro-2'-deoxy-5-ethyluridine
-
-
2,3'-anhydro-5-ethyluridine
-
competitive
2,5'-Anhydro-2'-deoxy-5-ethyluridine
-
-
2-deoxyglycosylthymine
-
-
3'-Azido-2',3'-dideoxy-5-ethyluridine
-
-
3'-Azido-2',3'-dideoxy-5-methyluridine
-
-
3'-Bromo-2',3'-dideoxy-5-ethyluridine
-
-
3'-Chloro-2',3'-dideoxy-5-ethyluridine
-
-
3'-Chloro-2',3'-dideoxy-5-methyluridine
-
-
3'-O-Acetyl-2,2'-anhydro-5-ethyluridine
-
-
3-((2-pyrrolidine-1-yl)ethyl)uracil
inhibits both enzymic activity and growth of Plasmodium falciparum
3-O-methyl-alpha-D-glucopyranose
-
-
5,5'-dithiobis(2-nitrobenzoic acid)
-
-
5-(3'-Benzyloxybenzyl)-1-[(1'-aminomethyl-2'-hydroxyethoxy)methyl]uracil
5-(Benzyloxybenzyloxybenzyl)acyluridine
-
-
-
5-(phenylthio)acyclouridine
5-Azauracil
-
reaction is inhibited in the direction of deoxyuridine synthesis more than in the direction of their cleavage at the same concentration of 5-azauracil
5-benzylacyclouridine
5-bromoacyclouridine
-
-
5-fluoro-2'-deoxyuridine
5-fluoroacyclouridine
-
-
5-iodoacyclouridine
-
-
5-m-benzyloxybenzyl acyclouridine
-
-
5-m-benzyloxybenzyl barbituric acid acyclonucleoside
-
-
5-phenylselenenylacyclouridine
-
-
5-phenylthioacyclouridine
-
-
5-Substituted 2,2'-anhydrouridine
6-Methyluracil
-
-
Acyclonucleoside analogues
-
consisting of 5- and 5,6-substituted uracils and different acyclic chains
-
Acyclothymidine
-
competitive
acyclouridine
-
competitive
alpha-D-ribose 1-phosphate
Arabinofuranosyl-5-ethyluracil
-
-
Benzylacyclouridines
Deoxyglucosylthymine
-
phosphorolysis of uridine and deoxyuridine, synthesis of uridine at concentrations of 0.10 mM, 0.018 mM and 0.14 mM, not: phosphorolysis of deoxyuridine or thymidine at 0.19 mM
deoxythymidine
-
-
guanidine hydrochloride
-
50% loss of activity at 1.04 M, only little residual activity between 2 and 6 M
iodoacetamide
-
-
iodoacetic acid
-
-
N-ethyl-5-phenylisoxazolium-3'-sulfonate
-
Woodward's reagent K
N-ethylmaleimide
-
-
o-Iodosobenzoate
-
-
p-chloromercuribenzoate
p-Mercuriphenylsulfonate
-
-
phosphate
Pyrimidine acyclonucleosides
-
competitive
-
ribose 1-phosphate
tetramethylene acyclouridine
-
-
thymidine 5-monophosphate
-
-
Uracil
uridine
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Triton X-100
-
0.1%, stimulates enzyme of isolated plasma membrane
uridine
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.13
2'-deoxyuridine
-
-
0.756
5'-deoxy-5-fluorouridine
-
-
0.1
5-bromodeoxyuridine
-
-
0.03
5-Bromouridine
-
-
0.427
5-fluoro-2'-deoxyuridine
pH 7.4, 37C
0.036 - 0.06
5-fluorouracil
0.024
5-fluorouridine
pH 7.4, 37C
0.07 - 4
5-methyluridine
0.02 - 0.087
alpha-D-ribose-1-phosphate
0.3 - 0.71
deoxyuridine
0.005
Inosine
pH 7.5, 25C
0.076 - 3.9
phosphate
0.017 - 0.14
ribose 1-phosphate
0.073 - 0.148
thymidine
0.06 - 0.485
Uracil
0.016 - 3.8
uridine
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
56
5-methyluridine
Aeropyrum pernix
-
pH 7.0, 90C
150
uridine
Aeropyrum pernix
-
pH 7.0, 90C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
230
5-methyluridine
Aeropyrum pernix
-
pH 7.0, 90C
3184
74
Inosine
Plasmodium falciparum
Q8I3X4
pH 7.5, 25C
167
0.306 - 240
uridine
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.027
1-((2-pyrrolidine-1-yl)ethyl)uracil
pH 7.5, 25C
0.0027
1-(1',3'-dihydroxy-2'-propoxy)methyl-5,6-tetramethyleneuracil
-
-
0.00007
1-(1',3'-dihydroxy-2'-propoxy)methyl-5-benzyluracil
-
-
0.109
2',3'-Dideoxy-5-ethyluridine
-
-
1.003
2'-deoxylyxofuranosyl-5-ethyluracil
-
-
0.000025 - 0.00007
2,2'-Anhydro-5-ethyluridine
0.014
2,3'-anhydro-5-ethyluridine
-
-
0.005
2-deoxyglycosylthymine
-
-
0.225
3'-Azido-2',3'-dideoxy-5-ethyluridine
-
-
0.056
3'-Azido-2',3'-dideoxy-5-methyluridine
-
-
0.448
3'-Bromo-2',3'-dideoxy-5-ethyluridine
-
-
0.21
3'-Chloro-2',3'-dideoxy-5-ethyluridine
-
-
0.361
3'-Chloro-2',3'-dideoxy-5-methyluridine
-
-
0.006
3-((2-pyrrolidine-1-yl)ethyl)uracil
pH 7.5, 25C
1.36
3-O-methyl-alpha-D-glucopyranose
-
-
0.000018
5-(3'-Benzyloxybenzyl)-1-[(1'-aminomethyl-2'-hydroxyethoxy)methyl]uracil
-
-
0.000098 - 0.0073
5-benzylacyclouridine
0.013
5-bromoacyclouridine
-
-
0.014
5-fluoroacyclouridine
-
-
0.03
5-iodoacyclouridine
-
-
0.00068
5-m-benzyloxybenzyl acyclouridine
-
-
0.003
Acyclothymidine
-
-
0.015
acyclouridine
-
-
0.034 - 3.5
alpha-D-ribose 1-phosphate
0.107
Arabinofuranosyl-5-ethyluracil
-
-
0.07 - 2.5
N-ethyl-5-phenylisoxazolium-3'-sulfonate
0.0088
tetramethylene acyclouridine
-
-
0.05 - 1.45
Uracil
0.047
uridine
-
-
additional information
additional information
-
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.44
substrate deoxyuridine, pH 6.5
2.75
substrate uridine, pH 7.5
7.7
purified recombinant enzyme
89.6
-
-
100 - 120
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.9
-
deoxynucleoside phosphorolysis
7.3
-
uridine phosphorolysis
7.5
with substrate uridine
7.6
recombinant enzyme
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
recombinant enzyme,m pH profile, overview
5.6 - 8.4
-
mutant UPL8, more than 60% of maximum activity within
5.8 - 9
-
pH 5.8: about 50% of activity maximum, pH 9.0: about 40% of activity maximum
6 - 8.2
-
wild-type, more than 60% of maximum activity within
6 - 8.5
pH dependence of enzyme activities with different substrates, overview
6.5 - 10.5
-
pH 6.5: about 50% of activity maximum, pH 10.5: about 65% of activity maximum
7 - 7.75
-
pH 6.5: about 70% of activity maximum, pH 8.5: about 25% of activity maximum
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
wild-type
60
-
mutant UPL8
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 80
-
40C: about 40% of activity maximum, 80C: about 10% of activity maximum
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
colon 26 tumor cells transplanted in BALB/c mice
Manually annotated by BRENDA team
-
brain, liver and heart
Manually annotated by BRENDA team
-
high activity
Manually annotated by BRENDA team
-
embryo
Manually annotated by BRENDA team
-
high activity
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
additional information
-
present in all human tissue and tumors
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
associated with intermediate filament vimentin in fibroblasts and colon 26 cells
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Actinobacillus succinogenes (strain ATCC 55618 / 130Z)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Shewanella oneidensis (strain MR-1)
Shewanella oneidensis (strain MR-1)
Shewanella oneidensis (strain MR-1)
Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio fischeri (strain ATCC 700601 / ES114)
Vibrio fischeri (strain ATCC 700601 / ES114)
Vibrio fischeri (strain ATCC 700601 / ES114)
Yersinia pseudotuberculosis serotype I (strain IP32953)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32000 - 35000
-
SDS-PAGE
43000
-
gel filtration
45000
-
gel filtration
56000
-
gel filtration
65000
-
gel filtration
80000
-
non-denaturing PAGE
102500
-
disc gel electrophoresis
110000
-
gel filtration
130000
-
gel filtration, native enzyme
160000
-
gel filtration
185300
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
isozyme UPP1, the N-terminus of the protein forms a strand-turn-strand structure bracketed by two short helices, structure, overview
hexamer
homodimer
monomer
octamer
-
8 * 22200, SDS-PAGE
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method
-
hanging-drop vapour-diffusion method, crystals of thymidine phosphate complex, 2'-deoxyuridine complex, 5-fluorouracil ribose 1-phosphate complex and native enzyme form
-
hanging-drop vapour-diffusion method, structure at 2.0 A resolution
-
hanging-drop vapour-diffusion method, structures of 5-benzylacyclouridine, 5-phenylthioacyclouridine, 5-phenylselenylacyclouridine, 5-m-benzyloxybenzyl acyclouridine and 5-m-benzyloxybenzyl barbituric acid acyclonucleoside bound to the active site of the enzyme, resolutions ranging from 1.95 to 2.3 A
-
free enzyme and enzyme in complex with inhibitor 5-benzylacyclouridine, 3 mg/ml protein in absence or presence of 1 mM inhibitor from 17% PEG 3350, 100 mM Bis-Tris buffer, pH 5.5, 300 mM KCl, and 30 mM MgCl2, or for the ligand-free ezyme crystals from 1.2 M (NH4)2SO4, 100 mM Bis-Tris buffer pH 5.5, with 1-2% MPD, with 2-3 mg/ml protein, X-ray diffraction structure determination and analysis at 2.3 A and 1.9 A resolution, respectively
in complex with 5-fluorouridine, to 2.3 A resolution. The dimeric enzyme is capable of a large hinge motion between its two domains, facilitating ligand exchange and explaining observed cooperativity between the two active sites in binding phosphate-bearing substrates. A loop toward the back end of the uracil binding pocket flexibly adjusts to the varying chemistry of different compounds through an induced-fit association mechanism
two crystallographic structures of human isoform UPP2 in distinctly active and inactive conformations, to 2.0 and 1.54 A resolution, respectively. The structures reveal that a conditional intramolecular disulfide bridge can form within the protein that dislocates critical phosphate-coordinating arginine residue R100 away from the active site, disabling the enzyme. The state of the disulfide bridge has further structural consequences for one face of the enzyme that suggest UPP2 may have additional functions in sensing and initiating cellular responses to oxidative stress
modeling of the inhibitors 1-((2-pyrrolidine-1-yl)ethyl)uracil and 3-((2-pyrrolidine-1-yl)ethyl)uracil into the active site of the protein, PDB entry 1NW4, by superposition of the uracil ring and the purine ring of Immucillin-H. Both compounds can fit adequately in the active site. In both cases the uracil base is predicted to be oriented in the nucleoside binding pocket by a pi-stacking similar to the purine base of Immucillin-H. The N1 of the uracil base in 1-((2-pyrrolidine-1-yl)ethyl)uracil and the N3 of the uracil base in 3-((2-pyrrolidine-1-yl)ethyl)uracil roughly superimpose with the C4 of Immucillin-H
complexed with 2,2-anhydrouridine, phosphate and potassium ions at 1.86 A resolution. The monomer is an alpha/beta-class polypeptide with a trilayer alpha/beta/alpha sandwich architecture. The potassium ion is located in the intermonomeric region of each homodimer on the local axis of second order of point group 32. The side chains of Glu49B and Ser73B and the carbonyl O atom of Ile69B in the B subunit, as well as symmetrical residues from the D subunit of the BD homodimer, coordinate K+. The residues in the phosphate binding site are Arg30B, Arg91B, Thr94B and Gly26B from the B subunit, and Arg48D from the D subunit
-
enzyme in complex with 5-fluorouracil, hanging-drop vapour-diffusion method, 0.5 ml of reservoir solution containing 0.34 ml 0.1 M Tris-maleate/NaOH buffer, pH 5.5, and 0.16 ml 40% w/v PEG 3350 is mixed with 2 ml protein solution containing 11.3 mg/ml enzyme in 10 mM Tris-HCl buffer, pH 7.3, 0.002 ml H2O, 0.0013 ml reservoir solution, 0.002 ml 100 mM 5-fluorouracil, and 0.0003 ml 2-propanol, 21C, 1-2 weeks, X-ray diffraction structure determination and analysis at 2.2 A resolution, modeling
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hanging drop vapour-diffusion method, 2.5 A resolution
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hanging-drop vapour-diffusion method with PEG as precipitant, 2.9 A resolution
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in complex with 5-fluorouridine, to 2.2 A resolution. The quaternary structure is represented by a hexamer comprised of six identical subunits. The packing of subunits in the hexamer can be described by the symmetry point group L33L2. The main structural and functional unit in the ligand-free state is a homodimer.The hexameric structure is formed by three homodimers with hydrophobic and hydrogen-bond interactions
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in complex with with the inhibitor 2,2'-anhydrouridine, the substrate phosphate, and with both the inhibitor 2,2'-anhydrouridine and the substrate phosphate, to 2.38, 1.5 and 1.75 A resolution, respectively. The presence of the phosphate ion in the phosphate-binding site substantially changes the orientations of the side chains of the amino-acid residues Arg30, Arg91, and Arg48 coordinated to this ion. The highly flexible loop L9 is unstable
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to a resolution of 1.9 A from crystals of the free form grown on earth, 1.6 A from crystals of the complex with uridine and 0.95 A from crystals of the free form grown under microgravity. All crystals belong to the space group P21 and have similar unit-cell parameters
free selenomethionine-labeled enzyme, or enzyme in complex with uridine, X-ray diffraction structure determination and analysis at 2.7 A and 1.44 A resolution, respectively
in complex with thymidine, crystals diffrat to 2.1 A resolution, space group P21
in silico model of the complex with 5-fluorouracil. The quaternary structure is represented by a hexamer comprised of six identical subunits. The packing of subunits in the hexamer can be described by the symmetry point group L33L2. The hexameric structure of the complex is stabilized by hydrophobic interactions and hydrogen bonds between the amino-acid residues of adjacent homodimers
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 - 9
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pH stability ranging from pH 3.0 to pH 9.0
726781
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
1 month, 20% loss of activity
65
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aglycone substrates, nucleoside substrates, phosphate or pentose 1-phosphate ester substrates stabilize against heat inactivation
75
-
1 h, 3.7% residual activity for wild-type, 80.2% residual activity for mutant UPL8
90
-
after incubation for 60 min at 90 C, the enzyme remains 100% active
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
aglycone substrates, nucleoside substrates, phosphate or pentose 1-phosphate ester substrates stabilize against heat inactivation
-
Ca2+ or EGTA stabilize the enzyme
much less stable in Tris buffer than in phosphate buffer
-
use of dithiothreitol and glycerol is necessary for stabilization during purification
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, stable for 6 months
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-20C, stable for at least 2 weeks
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-40C, 0.05 M potassium phosphate buffer, pH 7.0, 10 mM 2-mercaptoethanol, 1 mM EDTA, 10% loss of activity after 6 weeks
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-73C, stable for at least 3 months, purified enzyme
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-73C, stable for at least 6 months, crude extract
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5C, 90% loss of activity after 3-4 days
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
homogeneity
near homogeneity
-
partial
phosphorylase type I
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recombinant enzyme from Escherichia coli strain BL21(DE3) by hydrophobic interaction and anion exchange chromatography to 96% homogeneity
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recombinant N-terminally His6-tagged UPP1 from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant UP1 3.8fold from Escherichia coli strain Rosetta (DE3)
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Colo-320TP1 and C26A cells
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expression in Escherichia coli
expression in Escherichia coli as a fusion protein to glutathione-S-transferase
expression in Escherichia coli strain BL21(DE3)
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expression in Escherichia coli, the native apUP protein without fusion tags is actively expressed, and about 50% of the protein is found in the soluble fraction of the cell lysate
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expression of the N-terminally His6-tagged UPP1 in Escherichia coli strain BL21(DE3)
expression of UP1 in Escherichia coli strain Rosetta (DE3)
fusion protein with maltose-binding protein
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the peroxisome proliferator-activated receptor gamma coactivator-1alpha induces the enzyme in cancer cells via binding of a nuclear receptor, leading to enhanced antiproliferative activity of 5-deoxy-5-fluorouridine, overview. The activation is abolished by XCT790, i.e. 3-[4-(2,4-bis-trifluoromethylbenzyloxy)-3-methoxyphenyl]-2-cyano-N-(5-trifluoromethyl-1,3,4-thiadiazol-2-yl)acrylamide. Molecular mechanisms, overview
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C206_A207insGVPLC
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inactive and insoluble mutant protein
E196A
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complete loss of uridine phosphorylase activity
E198D
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complete loss of uridine phosphorylase activity
E198G
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complete loss of uridine phosphorylase activity
E198Q
-
complete loss of uridine phosphorylase activity
E79-E80insGVPLE
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inactive mutant protein
F162A
-
mutation causes a drastic decrease in uridine phosphorylase activity
G174_R175insRGTPG
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134% of the activity of the wild-type enzyme
H8A
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mutation lowers the activity by 20%
I102_N103insGVPHI
-
inactive and insoluble mutant protein
I69A
-
mutation does not decrease activity
I98_Q99insRGTPI
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inactive and insoluble mutant protein
K181_G182insGGTPK
-
67% of the activity of the wild-type enzyme
L9_G10insGVPHL
-
139% of the activity of the wild-type enzyme
M197A
-
low activity conserved
M197S
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low activity conserved
R30A
-
complete loss of uridine phosphorylase activity
R30K
-
very low activity
R91A
-
complete loss of uridine phosphorylase activity
R91K
-
very low activity
S159_D160insGGTPS
-
inactive mutant protein
S183_M184insMGYPS
-
54% of the activity of the wild-type enzyme
S183_M184insRGTPS
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117% of the activity of the wild-type enzyme
T12_K13insGVPLT
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132% of the activity of the wild-type enzyme
T52_W53insWGTPT
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inactive mutant protein
T67_G68insGGTPT
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inactive mutant protein
T94A
-
mutation causes a drastic decrease in uridine phosphorylase activity
V192_M193insMGYPV
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inactive mutant protein
V31_E32insGVPRV
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inactive and insoluble mutant protein
V42_K43insKGYPV
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as active as the wild-type enzyme
W196D
-
mutant enzyme is still partially active
Y195A
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increase in activity
Y195G
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mutation causes a drastic decrease in uridine phosphorylase activity
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dilution of the enzyme preincubated with 2 M guanidine hydrochloride results in partial recovery
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
UP12 is a target for development of enzyme inhibitors for cancer chemotherapy, design of inhibitors is intended to boost endogenous uridine levels to rescue normal tissues from the toxicity of fluoropyrimidine nucleoside chemotherapeutic agents, such as capecitabine and 5-fluorouracil.
medicine
synthesis
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