Information on EC 1.14.11.3 - pyrimidine-deoxynucleoside 2'-dioxygenase:

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The expected taxonomic range for this enzyme is: Eukaryota


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EC NUMBERCOMMENTARY
1.14.11.3-

RECOMMENDED NAMEGeneOntology No.
pyrimidine-deoxynucleoside 2'-dioxygenaseGO:0047080

REACTIONREACTION DIAGRAMCOMMENTARYORGANISM UNIPROT ACCESSION NO.LITERATURE
2'-deoxyuridine + 2-oxoglutarate + O2 = uridine + succinate + CO2
show the reaction diagram
----

REACTION TYPEORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
oxidation----
oxidative decarboxylation----
redox reaction----
reduction----

PATHWAYKEGG LinkMetaCyc Link
No entries in this field

SYSTEMATIC NAMEIUBMB 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.

SYNONYMSORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
deoxyuridine 2'-dioxygenase----
deoxyuridine 2'-hydroxylase----
JBP1Leishmania major, Leishmania tarentolae, Trypanosoma brucei--725475
JBP1Trypanosoma brucei 427---
JBP1Trypanosoma cruzi--725475
JBP2Leishmania major, Leishmania tarentolae, Trypanosoma brucei--725475
JBP2Trypanosoma brucei 427---
JBP2Trypanosoma cruzi--725475
pyrimidine deoxyribonucleoside 2'-hydroxylase----
thymidine 2'-dioxygenase----
thymidine 2'-hydroxylase----
thymidine 2-oxoglutarate dioxygenase----
thymidine dioxygenase----

CAS REGISTRY NUMBERCOMMENTARY
9076-89-5-

ORGANISMCOMMENTARYLITERATURESEQUENCE CODESEQUENCE DB SOURCE
Leishmania major-725475--Manually annotated by BRENDA team
Leishmania tarentolae-725475--Manually annotated by BRENDA team
Neurospora crassacell-free preparation; strain 1A439177--Manually annotated by BRENDA team
Neurospora crassastrain 1A439175, 439176--Manually annotated by BRENDA team
Neurospora crassastrain STA 4439172, 439174--Manually annotated by BRENDA team
Neurospora crassa 1Astrain 1A439175, 439176, 439177--Manually annotated by BRENDA team
Neurospora crassa STAstrain STA 4439172, 439174--Manually annotated by BRENDA team
Rhodotorula glutinis-439137, 439141--Manually annotated by BRENDA team
Rhodotorula glutinisstrain ATCC 2527439170--Manually annotated by BRENDA team
Trypanosoma bruceiline 221a725475--Manually annotated by BRENDA team
Trypanosoma brucei 427line 221a725475--Manually annotated by BRENDA team
Trypanosoma cruzi-725475--Manually annotated by BRENDA team

GENERAL INFORMATIONORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
evolutionLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-JBP1 and JBP2 are members of the Fe2+/2-OG dioxygenase family725475
evolutionTrypanosoma brucei 427-JBP1 and JBP2 are members of the Fe2+/2-OG dioxygenase family-
malfunctionLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-mutation of residues involved in coordinating Fe2+ inhibit iron binding and thymidine hydroxylation725475
malfunctionTrypanosoma brucei 427-mutation of residues involved in coordinating Fe2+ inhibit iron binding and thymidine hydroxylation-
metabolismLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-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 DNA725475
physiological functionLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-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 vivo725475
physiological functionTrypanosoma brucei 427-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-
metabolismTrypanosoma brucei 427-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-
additional informationLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-the N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity725475
additional informationTrypanosoma brucei 427-the N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity-

SUBSTRATEPRODUCT                      REACTION DIAGRAMORGANISM UNIPROT ACCESSION NO. COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5-bromodeoxyuridine + 2-oxoglutarate + O25-bromouridine + succinate + CO2
show the reaction diagram
Neurospora crassa, Neurospora crassa STA--439174--?
5-hydroxymethyldeoxyuridine + 2-oxoglutarate + O25-hydroxymethyluridine + succinate + CO2
show the reaction diagram
Neurospora crassa, Neurospora crassa STA--439174--?
thymidine + 2-oxoglutarate + O25-methyluridine + succinate + CO2
show the reaction diagram
Neurospora crassa--439174---
thymidine + 2-oxoglutarate + O25-methyluridine + succinate + CO2
show the reaction diagram
Neurospora crassa, Neurospora crassa 1A-conversion to the ribonucleotide prior to its utilization for DNA synthesis439176-439176?
thymidine + 2-oxoglutarate + O25-hydroxymethyluridine + succinate + CO2
show the reaction diagram
Trypanosoma brucei, Trypanosoma cruzi, Leishmania tarentolae, Leishmania major-JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner725475--?
thymidine + 2-oxoglutarate + O25-hydroxymethyluridine + succinate + CO2
show the reaction diagram
Trypanosoma brucei, Trypanosoma cruzi, Leishmania tarentolae, Leishmania major-telomeric duplex DNA substrate, JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner725475mass spectrometric product determination-?
thymidine + 2-oxoglutarate + O25-hydroxymethyluridine + succinate + CO2
show the reaction diagram
Trypanosoma brucei 427-JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner725475--?
thymidine + 2-oxoglutarate + O25-hydroxymethyluridine + succinate + CO2
show the reaction diagram
Trypanosoma brucei 427-telomeric duplex DNA substrate, JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner725475mass spectrometric product determination-?
thymidylate + 2-oxoglutarate + O25-methyluridine 5'-phosphate + succinate + CO2
show the reaction diagram
Neurospora crassa, Neurospora crassa STA--439174--?
6-azathymidine + 2-oxoglutarate + O25-mehyluridine + succinate + CO2
show the reaction diagram
Neurospora crassa, Neurospora crassa STA--439174--?
additional information?-Neurospora crassa-only pyrimidine deoxyribonucleosides with oxygen at carbon 2 and 4 are active439174---
additional information?-Trypanosoma brucei, Trypanosoma cruzi, Leishmania tarentolae, Leishmania major, Trypanosoma brucei 427-thymine in the context of single stranded DNA substrate, rather than duplex DNA, is not hydroxylated725475---
additional information?-Neurospora crassa STA-only pyrimidine deoxyribonucleosides with oxygen at carbon 2 and 4 are active439174---

NATURAL SUBSTRATESNATURAL PRODUCTSREACTION DIAGRAMORGANISM UNIPROT ACCESSION NO.COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
thymidine + 2-oxoglutarate + O25-methyluridine + succinate + CO2
show the reaction diagram
Neurospora crassa-conversion to the ribonucleotide prior to its utilization for DNA synthesis439176-439176?
thymidine + 2-oxoglutarate + O25-hydroxymethyluridine + succinate + CO2
show the reaction diagram
Trypanosoma brucei, Trypanosoma cruzi, Leishmania tarentolae, Leishmania major-JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner725475--?
thymidine + 2-oxoglutarate + O25-methyluridine + succinate + CO2
show the reaction diagram
Neurospora crassa 1A-conversion to the ribonucleotide prior to its utilization for DNA synthesis439176-439176?
thymidine + 2-oxoglutarate + O25-hydroxymethyluridine + succinate + CO2
show the reaction diagram
Trypanosoma brucei 427-JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe2+-, 2-oxoglutarate-, and O2-dependent manner725475--?

COFACTORORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATUREIMAGE
No entries in this field

METALS and IONS ORGANISM UNIPROT ACCESSION NO.COMMENTARY LITERATURE
Fe2+Rhodotorula glutinis--439141
Fe2+Neurospora crassa--439174, 439175, 439176, 439177
Fe2+Leishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-dependent on725475

INHIBITORSORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
1,10-phenanthrolineNeurospora crassa-at 0.02 mM complete inhibition439174 2D-image
2,4-pyridinedicarboxylic acid hydrateLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-competitive inhibition725475-
2-ketoadipateNeurospora crassa-38% inhibition at 2.5 mM439174 2D-image
2-ketopimelateNeurospora crassa-26% inhibition at 2.5 mM439174 2D-image
3-ketoadipateNeurospora crassa-50% inhibition at 2.5 mM439174 2D-image
3-oxoglutarateNeurospora crassa-27% inhibition at 2.5 mM439174 2D-image
Co2+Neurospora crassa-95% inhibition at 0.25 mM439174 2D-image
Cu2+Neurospora crassa-95% inhibition at 0.25 mM439174 2D-image
DiglycolateNeurospora crassa-18% inhibition at 2.5 mM439174 2D-image
dimethyloxoglycineLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-competitive inhibition725475-
glutamateNeurospora crassa-20% inhibition at 2.5 mM439174 2D-image
iminodiacetateNeurospora crassa-28% inhibition at 2.5 mM439174 2D-image
Mn2+Neurospora crassa-60% inhibition at 0.25 mM439174 2D-image
N2Neurospora crassa-complete inhibition by exclusion of oxygen439176 2D-image
Ni2+Neurospora crassa-95% inhibition at 0.25 mM439174 2D-image
ThiodiglycolateNeurospora crassa-24% inhibition at 2.5 mM439174 2D-image
Zn2+Neurospora crassa-95% inhibition at 0.25 mM439174 2D-image

ACTIVATING COMPOUNDORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
ascorbateRhodotorula glutinis-no enzyme activity detected when omitted from standard incubation mixture439141 2D-image
ascorbateNeurospora crassa-3fold activation at 5 mM439174 2D-image
ascorbateNeurospora crassa--439175, 439176, 439177 2D-image
ascorbateLeishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi--725475 2D-image
catalaseRhodotorula glutinis-30% activation at 0.33 mg per ml catalase439141-
catalaseNeurospora crassa-1.5fold activation at 2 mg per ml439174-
catalaseNeurospora crassa--439175-

KM VALUE [mM]KM VALUE [mM] MaximumSUBSTRATEORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
0.3-2-oxoglutarateNeurospora crassa--439174 2D-image
0.15-5-bromodeoxyuridineNeurospora crassa--439174 2D-image
0.29-5-HydroxymethyldeoxyuridineNeurospora crassa--439174 2D-image
0.29-6-AzathymidineNeurospora crassa--439174 2D-image
0.19-DeoxyuridineNeurospora crassa--439174 2D-image
0.45-Fe2+Neurospora crassa-at pH 7.2 in 50 mM phosphate buffer439174-
0.09-thymidineNeurospora crassa--439174 2D-image
0.07-thymidylateNeurospora crassa--439174 2D-image

TURNOVER NUMBER [1/s] TURNOVER NUMBER MAXIMUM[1/s] SUBSTRATEORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

kcat/KM VALUE [1/mMs-1]kcat/KM VALUE [1/mMs-1] MaximumSUBSTRATEORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

Ki VALUE [mM]Ki VALUE [mM] MaximumINHIBITORORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

IC50 VALUE [mM]IC50 VALUE [mM] MaximumINHIBITORORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

SPECIFIC ACTIVITY [µmol/min/mg] SPECIFIC ACTIVITY MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
0.053-Neurospora crassa-with thymidine as substrate439175
0.35-Rhodotorula glutinis--439170
0.97-Rhodotorula glutinis--439137

pH OPTIMUMpH MAXIMUMORGANISM UNIPROT ACCESSION NO. COMMENTARYLITERATURE
6.5-Neurospora crassa--439174
8-Leishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-assay at725475

pH RANGEpH RANGE MAXIMUMORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

TEMPERATURE OPTIMUMTEMPERATURE OPTIMUM MAXIMUMORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
37-Leishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma cruzi-assay at725475

TEMPERATURE RANGE TEMPERATURE MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

pI VALUEpI VALUE MAXIMUMORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

SOURCE TISSUE ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE SOURCE
bloodstream formTrypanosoma brucei--725475Manually annotated by BRENDA team
bloodstream formTrypanosoma brucei 427---Manually annotated by BRENDA team
metacyclic formLeishmania tarentolae-infective725475Manually annotated by BRENDA team
promastigoteLeishmania major--725475Manually annotated by BRENDA team

LOCALIZATION ORGANISM UNIPROT ACCESSION NO. COMMENTARY GeneOntology No. LITERATURE SOURCE
No entries in this field

PDBSCOPCATHORGANISM
No entries in this field

MOLECULAR WEIGHT MOLECULAR WEIGHT MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
47000-Neurospora crassa-gel filtration439172, 439174
64600-Rhodotorula glutinis-gel filtration439137

SUBUNITS ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
monomerNeurospora crassa-1 * 46000, SDS-PAGE439172
monomerNeurospora crassa STA-1 * 46000, SDS-PAGE-

POSTTRANSLATIONAL MODIFICATION ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

Crystallization/COMMENTARY ORGANISM UNIPROT ACCESSION NO. LITERATURE
No entries in this field

pH STABILITYpH STABILITY MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

TEMPERATURE STABILITYTEMPERATURE STABILITY MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARYLITERATURE
No entries in this field

GENERAL STABILITYORGANISM UNIPROT ACCESSION NO.LITERATURE
No entries in this field

ORGANIC SOLVENT ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

OXIDATION STABILITY ORGANISM UNIPROT ACCESSION NO. LITERATURE
No entries in this field

STORAGE STABILITY ORGANISM UNIPROT ACCESSION NO. LITERATURE
No entries in this field

Purification/COMMENTARY ORGANISM UNIPROT ACCESSION NO. LITERATURE
-Neurospora crassa-439172
-Rhodotorula glutinis-439137
partial purificationRhodotorula glutinis-439170
recombinant His-tagged JBP1 from Escherichia coli strain BL21-DE3 T1R by metal affinty chromatographyTrypanosoma cruzi-725475

Cloned/COMMENTARY ORGANISM UNIPROT ACCESSION NO. LITERATURE
recombinant expression of His-tagged JBP1 in Escherichia coli strain BL21-DE3 T1RTrypanosoma cruzi-725475

EXPRESSION ORGANISM UNIPROT ACCESSION NO. LITERATURE
No entries in this field

ENGINEERINGORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
additional informationLeishmania major, Leishmania tarentolae, Trypanosoma brucei-mutation of the two conserved metal binding ligands of dioxygenases JBP1 and JBP2 results in the loss of Fe2+ binding and inability to hydroxylate thymidine725475
additional informationTrypanosoma brucei 427-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 informationTrypanosoma cruzi-mutation of the two conserved metal binding ligands of dioxygenases JBP1 and JBP2 results in the loss of Fe2+ binding and inability to hydroxylate thymidine725475

Renatured/COMMENTARYORGANISM UNIPROT ACCESSION NO.LITERATURE
No entries in this field

APPLICATIONORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

REF. AUTHORS TITLE JOURNAL VOL. PAGES YEAR ORGANISM (UNIPROT ACCESSION NO.)LINK TO PUBMEDSOURCE
439137Warn-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 glutinisJ. Biol. Chem.25810551-105571983Rhodotorula glutinis PubMed
439141Wondrack, L.M.; Hsu, C.A.; Abbott, M.T.Thymine 7-hydroxylase and pyrimidine desoxyribonucleoside 2'-hydroxylase activities in Rhodotorula glutinisJ. Biol. Chem.2536511-65151978Rhodotorula glutinis PubMed
439170Stubbe, J.Identification of two alpha-ketoglutarate-dependent dioxygenases in extracts of Rhodotorula glutinis catalyzing deoxyuridine hydroxylationJ. Biol. Chem.2609972-99751985Rhodotorula glutinis PubMed
439172Holme, E.Purification of thymidine 2'-hydroxylase from Neurospora crassaActa Chem. Scand.37743-7451983Neurospora crassa, Neurospora crassa STA PubMed
439174Bankel, L.; Lindstedt, G.; Lindstedt, S.Thymidine 2-hydroxylation in Neurospora crassaJ. Biol. Chem.2476128-61341972Neurospora crassa, Neurospora crassa STA PubMed
439175Liu, 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 acidBiochemistry112172-21761972Neurospora crassa 1A, Neurospora crassa PubMed
439176Shaffer, P.M.; McCroskey, R.P.; Abbott, M.T.Substrate specificity of the hydroxylase reaction in which thymidine is converted to thymine ribonucleosideBiochim. Biophys. Acta258387-3941972Neurospora crassa 1A, Neurospora crassa PubMed
439177Shaffer, 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 deoxyriboseBiochem. Biophys. Res. Commun.33806-8111968Neurospora crassa 1A, Neurospora crassa PubMed
725475Cliffe, 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 DNAJ. Biol. Chem.28719886-198952012Leishmania major, Leishmania tarentolae, Trypanosoma brucei, Trypanosoma brucei 427, Trypanosoma cruzi PubMed

LINKS TO OTHER DATABASES (specific for EC-Number 1.14.11.3)
ExplorEnz
ExPASy
KEGG
MetaCyc
NCBI: PubMed, Protein, Nucleotide, Structure, Genome, OMIM
IUBMB Enzyme Nomenclature
PROSITE Database of protein families and domains
SYSTERS
Protein Mutant Database
InterPro (database of protein families, domains and functional sites)