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Information on EC 1.14.11.3 - pyrimidine-deoxynucleoside 2'-dioxygenase
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EC Tree
1.14.11.3 pyrimidine-deoxynucleoside 2'-dioxygenaseIUBMB Comments
Requires Fe(II) and ascorbate. Also acts on thymidine. cf. EC 1.14.11.10, pyrimidine-deoxynucleoside 1'-dioxygenase.
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Word Map
- 1.14.11.3
- thymine
- alpha-ketoglutarate
-
7-hydroxylase
- ascorbate
-
rhodotorula
- nidulans
- co2
- uracil
-
salvage
- 5-hydroxymethyluracil
- crassa
- neurospora
- glutinis
The enzyme appears in viruses and cellular organisms
Synonyms
pyrimidine deoxyribonucleoside 2'-hydroxylase, deoxyuridine 2'-hydroxylase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
deoxyuridine 2'-dioxygenase
-
-
-
-
deoxyuridine 2'-hydroxylase
-
-
-
-
JBP1
JBP2
pyrimidine deoxyribonucleoside 2'-hydroxylase
-
-
-
-
thymidine 2'-dioxygenase
-
-
-
-
thymidine 2'-hydroxylase
-
-
-
-
thymidine 2-oxoglutarate dioxygenase
-
-
-
-
thymidine dioxygenase
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-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2'-deoxyuridine + 2-oxoglutarate + O2 = uridine + succinate + CO2
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-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
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-
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oxidative decarboxylation
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-
-
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redox reaction
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-
-
-
reduction
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
2'-deoxyuridine,2-oxoglutarate:oxygen oxidoreductase (2'-hydroxylating)
Requires Fe(II) and ascorbate. Also acts on thymidine. cf. EC 1.14.11.10, pyrimidine-deoxynucleoside 1'-dioxygenase.
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CAS REGISTRY NUMBER
COMMENTARY
9076-89-5
-
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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
5-hydroxymethyldeoxyuridine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
5-bromodeoxyuridine + 2-oxoglutarate + O2
5-bromouridine + succinate + CO2
-
-
-
-
?
5-bromodeoxyuridine + 2-oxoglutarate + O2
5-bromouridine + succinate + CO2
-
-
-
-
?
5-hydroxymethyldeoxyuridine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
-
-
-
?
5-hydroxymethyldeoxyuridine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
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-
-
-
?
6-azathymidine + 2-oxoglutarate + O2
5-mehyluridine + succinate + CO2
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-
-
-
?
6-azathymidine + 2-oxoglutarate + O2
5-mehyluridine + succinate + CO2
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-
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
telomeric duplex DNA substrate, JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
mass spectrometric product determination
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
telomeric duplex DNA substrate, JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
mass spectrometric product determination
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
telomeric duplex DNA substrate, JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
mass spectrometric product determination
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
telomeric duplex DNA substrate, JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
mass spectrometric product determination
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
telomeric duplex DNA substrate, JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
mass spectrometric product determination
-
?
thymidine + 2-oxoglutarate + O2
5-methyluridine + succinate + CO2
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-
-
-
?
thymidine + 2-oxoglutarate + O2
5-methyluridine + succinate + CO2
-
conversion to the ribonucleotide prior to its utilization for DNA synthesis
-
?
thymidine + 2-oxoglutarate + O2
5-methyluridine + succinate + CO2
-
conversion to the ribonucleotide prior to its utilization for DNA synthesis
-
?
thymidylate + 2-oxoglutarate + O2
5-methyluridine 5'-phosphate + succinate + CO2
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-
-
-
?
thymidylate + 2-oxoglutarate + O2
5-methyluridine 5'-phosphate + succinate + CO2
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-
-
-
?
additional information
?
-
-
thymine in the context of single stranded DNA substrate, rather than duplex DNA, is not hydroxylated
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-
?
additional information
?
-
-
thymine in the context of single stranded DNA substrate, rather than duplex DNA, is not hydroxylated
-
-
?
additional information
?
-
-
only pyrimidine deoxyribonucleosides with oxygen at carbon 2 and 4 are active
-
-
?
additional information
?
-
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only pyrimidine deoxyribonucleosides with oxygen at carbon 2 and 4 are active
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-
?
additional information
?
-
-
thymine in the context of single stranded DNA substrate, rather than duplex DNA, is not hydroxylated
-
-
?
additional information
?
-
-
thymine in the context of single stranded DNA substrate, rather than duplex DNA, is not hydroxylated
-
-
?
additional information
?
-
-
thymine in the context of single stranded DNA substrate, rather than duplex DNA, is not hydroxylated
-
-
?
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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
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-hydroxymethyluridine + succinate + CO2
-
JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner
-
-
?
thymidine + 2-oxoglutarate + O2
5-methyluridine + succinate + CO2
-
conversion to the ribonucleotide prior to its utilization for DNA synthesis
-
?
thymidine + 2-oxoglutarate + O2
5-methyluridine + succinate + CO2
-
conversion to the ribonucleotide prior to its utilization for DNA synthesis
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ascorbate
-
no enzyme activity detected when omitted from standard incubation mixture
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
evolution
-
JBP1 and JBP2 are members of the Fe2+/2-OG dioxygenase family
malfunction
-
mutation of residues involved in coordinating Fe2+ inhibit iron binding and thymidine hydroxylation
malfunction
-
mutation of residues involved in coordinating Fe2+ inhibit iron binding and thymidine hydroxylation
malfunction
-
mutation of residues involved in coordinating Fe2+ inhibit iron binding and thymidine hydroxylation
malfunction
-
mutation of residues involved in coordinating Fe2+ inhibit iron binding and thymidine hydroxylation
malfunction
-
mutation of residues involved in coordinating Fe2+ inhibit iron binding and thymidine hydroxylation
-
metabolism
-
JBP1 and JBP2 utilize 2-oxoglutarate and O2 as co-substrate to hydroxylate T-residues in dsDNA, releasing succinate and CO2 as byproducts. The intermediate hmU is then glycosylated by an unknown glucosyltransferase forming base J, two-step base J-biosynthesis pathway of modifying T-residues in kinetoplastid DNA
metabolism
-
JBP1 and JBP2 utilize 2-oxoglutarate and O2 as co-substrate to hydroxylate T-residues in dsDNA, releasing succinate and CO2 as byproducts. The intermediate hmU is then glycosylated by an unknown glucosyltransferase forming base J, two-step base J-biosynthesis pathway of modifying T-residues in kinetoplastid DNA
metabolism
-
JBP1 and JBP2 utilize 2-oxoglutarate and O2 as co-substrate to hydroxylate T-residues in dsDNA, releasing succinate and CO2 as byproducts. The intermediate hmU is then glycosylated by an unknown glucosyltransferase forming base J, two-step base J-biosynthesis pathway of modifying T-residues in kinetoplastid DNA
metabolism
-
JBP1 and JBP2 utilize 2-oxoglutarate and O2 as co-substrate to hydroxylate T-residues in dsDNA, releasing succinate and CO2 as byproducts. The intermediate hmU is then glycosylated by an unknown glucosyltransferase forming base J, two-step base J-biosynthesis pathway of modifying T-residues in kinetoplastid DNA
metabolism
-
JBP1 and JBP2 utilize 2-oxoglutarate and O2 as co-substrate to hydroxylate T-residues in dsDNA, releasing succinate and CO2 as byproducts. The intermediate hmU is then glycosylated by an unknown glucosyltransferase forming base J, two-step base J-biosynthesis pathway of modifying T-residues in kinetoplastid DNA
-
physiological function
-
the enzyme regulating the hydroxylation of specific T-residues along the chromosome is critical for the control of trypanosome gene expression. JBP activity is regulated by oxygen levels in vivo
physiological function
-
the enzyme regulating the hydroxylation of specific T-residues along the chromosome is critical for the control of trypanosome gene expression. JBP activity is regulated by oxygen levels in vivo
physiological function
-
the enzyme regulating the hydroxylation of specific T-residues along the chromosome is critical for the control of trypanosome gene expression. JBP activity is regulated by oxygen levels in vivo
physiological function
-
the enzyme regulating the hydroxylation of specific T-residues along the chromosome is critical for the control of trypanosome gene expression. JBP activity is regulated by oxygen levels in vivo
physiological function
-
the enzyme regulating the hydroxylation of specific T-residues along the chromosome is critical for the control of trypanosome gene expression. JBP activity is regulated by oxygen levels in vivo
-
additional information
-
the N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity
additional information
-
the N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity
additional information
-
the N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity
additional information
-
the N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity
additional information
-
the N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
mutation of the two conserved metal binding ligands of dioxygenases JBP1 and JBP2 results in the loss of Fe2+ binding and inability to hydroxylate thymidine
additional information
-
mutation of the two conserved metal binding ligands of dioxygenases JBP1 and JBP2 results in the loss of Fe2+ binding and inability to hydroxylate thymidine
additional information
-
mutation of the two conserved metal binding ligands of dioxygenases JBP1 and JBP2 results in the loss of Fe2+ binding and inability to hydroxylate thymidine
additional information
-
mutation of the two conserved metal binding ligands of dioxygenases JBP1 and JBP2 results in the loss of Fe2+ binding and inability to hydroxylate thymidine
-
additional information
-
mutation of the two conserved metal binding ligands of dioxygenases JBP1 and JBP2 results in the loss of Fe2+ binding and inability to hydroxylate thymidine
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged JBP1 from Escherichia coli strain BL21-DE3 T1R by metal affinty chromatography
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression of His-tagged JBP1 in Escherichia coli strain BL21-DE3 T1R
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Warn-Cramer, B.J.; Macrander, L.A.; Abbott, M.T.
Markedly different ascorbate dependencies of the sequential alpha-ketoglutarate dioxygenase reactions catalyzed by an essentially homogeneous thymine 7-hydroxylase from Rhodotorula glutinis
J. Biol. Chem.
258
10551-10557
1983
Rhodotorula glutinis
brenda
Wondrack, L.M.; Hsu, C.A.; Abbott, M.T.
Thymine 7-hydroxylase and pyrimidine desoxyribonucleoside 2'-hydroxylase activities in Rhodotorula glutinis
J. Biol. Chem.
253
6511-6515
1978
Rhodotorula glutinis
brenda
Stubbe, J.
Identification of two alpha-ketoglutarate-dependent dioxygenases in extracts of Rhodotorula glutinis catalyzing deoxyuridine hydroxylation
J. Biol. Chem.
260
9972-9975
1985
Rhodotorula glutinis
brenda
Holme, E.
Purification of thymidine 2'-hydroxylase from Neurospora crassa
Acta Chem. Scand.
37
743-745
1983
Neurospora crassa, Neurospora crassa STA 4
brenda
Bankel, L.; Lindstedt, G.; Lindstedt, S.
Thymidine 2-hydroxylation in Neurospora crassa
J. Biol. Chem.
247
6128-6134
1972
Neurospora crassa, Neurospora crassa STA 4
brenda
Liu, C.K.; Shaffer, P.M.; Slaughter, R.S.; McCroskey, R.P.; Abbott, M.T.
Stoichiometry of the pyrimidine deoxyribonucleoside 2-hydroxylase reaction and of the conversions of 5-hydroxymethyluracil to 5-formyluracil and of the latter to uracil-5-carboxylic acid
Biochemistry
11
2172-2176
1972
Neurospora crassa, Neurospora crassa 1A
brenda
Shaffer, P.M.; McCroskey, R.P.; Abbott, M.T.
Substrate specificity of the hydroxylase reaction in which thymidine is converted to thymine ribonucleoside
Biochim. Biophys. Acta
258
387-394
1972
Neurospora crassa, Neurospora crassa 1A
brenda
Shaffer, P.M.; McCroskey, R.P.; Palmatier, R.D.; Midgett, R.J.; Abbott, M.T.
The cell-free conversion of a deoxyribonucleoside to a ribonucleoside without detachment of the deoxyribose
Biochem. Biophys. Res. Commun.
33
806-811
1968
Neurospora crassa, Neurospora crassa 1A
brenda
Cliffe, L.J.; Hirsch, G.; Wang, J.; Ekanayake, D.; Bullard, W.; Hu, M.; Wang, Y.; Sabatini, R.
JBP1 and JBP2 proteins are Fe2+/2-oxoglutarate-dependent dioxygenases regulating hydroxylation of thymidine residues in trypanosome DNA
J. Biol. Chem.
287
19886-19895
2012
Leishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi, Trypanosoma brucei 427
brenda
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