Information on EC 2.7.1.78 - polynucleotide 5'-hydroxyl-kinase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.7.1.78
-
RECOMMENDED NAME
GeneOntology No.
polynucleotide 5'-hydroxyl-kinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phopho group transfer
phospho group transfer
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:5'-dephosphopolynucleotide 5'-phosphotransferase
Also acts on 5'-dephospho-RNA 3'-mononucleotides.
CAS REGISTRY NUMBER
COMMENTARY hide
37211-65-7
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
from infected Escherichia coli
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
chinese hamster lung cells
-
-
Manually annotated by BRENDA team
expression in Escherichia coli with His10-tag
-
-
Manually annotated by BRENDA team
expression in Escherichia coli with His10-tag
-
-
Manually annotated by BRENDA team
no activity in bacteriophage T1
-
-
-
Manually annotated by BRENDA team
no activity in bacteriophage T5
-
-
-
Manually annotated by BRENDA team
no activity in Escherichia coli
-
-
-
Manually annotated by BRENDA team
infecting Rhodothermus marinus, bifunctional enzyme with 5-kinase domain and 3-phosphohydrolase domain
-
-
Manually annotated by BRENDA team
synthetic ribozyme
class I polynucleotide kinase
-
-
Manually annotated by BRENDA team
trifunctional enzyme with RNA ligase, polynucleotide 5'-kinase, and polynucleotide 3'-phosphatase activities
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP + 5'-HO-AUCACGCUUpCp
?
show the reaction diagram
-
-
-
-
r
ATP + (AG)10GGCCC-fluorescein
?
show the reaction diagram
-
-
-
?
ATP + (AG)10GGCCC-tetramethylrhodamine
?
show the reaction diagram
-
-
-
?
ATP + 2'(3')-ribonucleotides
?
show the reaction diagram
ATP + 3'-carboxyfluorescein-labeled DNA/complementary DNA hybrid
?
show the reaction diagram
-
-
-
-
?
ATP + 3'-CMP
ADP + pCp
show the reaction diagram
ATP + 5'-CACTGTAACTGATCCTGCCGCTATG-3'
?
show the reaction diagram
-
-
-
-
?
ATP + 5'-CATAGCGGCAGGATCAGTTACAGTG-3'
?
show the reaction diagram
-
-
-
-
?
ATP + 5'-CCTAACCCTTTCTTTCTTTTCAGGGTTAGGGTTAGGGTTAGGG-3'
?
show the reaction diagram
-
-
-
-
?
ATP + 5'-CTGGCGCTTGATGGTATTTTTACCATCAAGCGCCAG-3'
?
show the reaction diagram
-
-
-
-
?
ATP + 5'-dephospho-DNA
ADP + 5'-phospho-DNA
show the reaction diagram
ATP + 5'-dephospho-GAAAA-RNA
ADP + 5'-phospho-GAAAA-RNA
show the reaction diagram
-
-
-
?
ATP + 5'-dephospho-GC-RNA
ADP + 5'-phospho-GC-RNA
show the reaction diagram
-
-
-
?
ATP + 5'-dephospho-RNA
ADP + 5'-phospho-RNA
show the reaction diagram
ATP + 5'-dsRNA
ADP + 5'-phospho-dsRNA
show the reaction diagram
-
-
-
-
?
ATP + 5'-GGCAACAT
?
show the reaction diagram
-
-
-
-
?
ATP + 5'-HO-CCGACCAACGAAGGT
?
show the reaction diagram
-
-
-
-
r
ATP + 5'-OH DNA
ADP + 5'-phospho-DNA
show the reaction diagram
-
-
-
r
ATP + 5'-OH RNA
ADP + 5'-phospho-RNA
show the reaction diagram
preference for RNA substrates
-
-
r
ATP + d(A20)
ADP + 5'-phospho-d(A20)
show the reaction diagram
-
-
-
-
?
ATP + deoxynucleoside 3'-phosphate
ADP + deoxynucleoside 3',5'-diphosphate
show the reaction diagram
-
-
-
-
?
ATP + GGGCC(AG)10GGCCC-fluorescein
?
show the reaction diagram
-
-
-
?
ATP + GGGCC(AG)10GGCCC-tetramethylrhodamine
?
show the reaction diagram
-
-
-
?
ATP + GGGCC(AG)12GGCCC-fluorescein
?
show the reaction diagram
-
-
-
?
ATP + GGGCC(AG)8GGCCC-fluorescein
?
show the reaction diagram
-
-
-
?
ATP + GGGGC(AG)10GCCCC-fluorescein
?
show the reaction diagram
-
-
-
?
ATP + GGGGC(AG)10GCCCC-tetramethylrhodamine
?
show the reaction diagram
-
-
-
?
ATP + GGGGG(AG)10CCCCC-fluorescein
?
show the reaction diagram
-
-
-
?
ATP + GGGGG(AG)10CCCCC-tetramethylrhodamine
?
show the reaction diagram
-
-
-
?
ATP + magnetite microspheres coated with TiO2-DNA complex
?
show the reaction diagram
-
-
-
-
?
ATP + nucleoside-3'-monophosphate
ADP + nucleoside-3',5'-diphosphate
show the reaction diagram
ATP + r(A20)
ADP + 5'-phospho-r(A20)
show the reaction diagram
-
-
-
-
?
ATP + synthetic oligonucleotide
ADP + oligonucleotide 5'-phosphate
show the reaction diagram
beta,gamma-imidoadenylyl 5'-triphosphate + 5'-phospho-DNA
beta,gamma-imidoadenylyl 5'-tetraphosphate + 5'-dephospho-DNA
show the reaction diagram
CTP + 5'-dephospho-DNA
CDP + 5'-phospho-DNA
show the reaction diagram
CTP + 5'-dephospho-RNA
CDP + 5'-phospho-RNA
show the reaction diagram
dATP + 5'-dephospho-DNA
dADP + 5'-phospho-DNA
show the reaction diagram
-
-
-
?
dATP + 5'-dephospho-RNA
dADP + 5'-phospho-RNA
show the reaction diagram
-
-
-
-
r
GTP + 5'-dephospho-DNA
GDP + 5'-phospho-DNA
show the reaction diagram
GTP + 5'-dephospho-RNA
GDP + 5'-phospho-RNA
show the reaction diagram
-
-
-
-
r
TTP + 5'-dephospho-DNA
TDP + 5'-phospho-DNA
show the reaction diagram
-
-
-
?
UTP + 5'-dephospho-DNA
UDP + 5'-phospho-DNA
show the reaction diagram
UTP + 5'-dephospho-RNA
UDP + 5'-phospho-RNA
show the reaction diagram
-
-
-
-
r
[gamma-S]ATP + 5'-dephospho-RNA
[gamma-S]ADP + 5'-phospho-RNA
show the reaction diagram
-
-
-
?
[gamma-S]ATP + 5'-OH-(ribonucleotide)7
[gamma-S]ADP + 5'-phospho-(ribonucleotide)7
show the reaction diagram
[gamma-S]GTP + 5'-dephospho-RNA
[gamma-S]GDP + 5'-phospho-RNA
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
ATP + 5'-dephospho-DNA
ADP + 5'-phospho-DNA
show the reaction diagram
ATP + 5'-dephospho-RNA
ADP + 5'-phospho-RNA
show the reaction diagram
ATP + 5'-dsRNA
ADP + 5'-phospho-dsRNA
show the reaction diagram
-
-
-
-
?
ATP + 5'-OH DNA
ADP + 5'-phospho-DNA
show the reaction diagram
Q57936
-
-
-
r
ATP + 5'-OH RNA
ADP + 5'-phospho-RNA
show the reaction diagram
Q57936
preference for RNA substrates
-
-
r
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4-(3-bromo-8-chloro-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl)-N1-cyclohexyl-N2-[2-(1H-imidazol-4-yl)ethyl]piperazine-1,2-dicarboxamide
4-(3-bromo-8-chloro-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl)-N1-cyclohexyl-N2-[3-(1H-imidazol-4-yl)propyl]piperazine-1,2-dicarboxamide
-
-
ADP
-
reverse reaction
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Divalent cations
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-(1-hydroxyundecyl)-1-(4-nitrophenylamino)-6-phenyl-6,7a-dihydro-1H-pyrrolo[3,4-b]pyridine-5,7(2H,4aH)-dione
2-(hydroxy(3,4,5-trimethoxyphenyl)methyl)-1-(4-nitrophenylamino)-6-phenyl-6,7a-dihydro-1H-pyrrolo[3,4-b]pyridine-5,7(2H,4aH)-dione
-
A6B4C3
2-(hydroxy(phenyl)methyl)-1-(4-nitrophenylamino)-6-phenyl-6,7a-dihydro-1H-pyrrolo[3,4-b]pyridine-5,7(2H,4aH)-dione
-
A1B4C3
2-(hydroxy(thiophen-2-yl)methyl)-6-methyl-1-(phenylamino)-6,7a-dihydro-1H-pyrrolo[3,4-b]pyridine-5,7(2H,4aH)-dione
-
A39B1C2
5'-AMP
-
weak
5'-Hydroxyl poly(I)
-
in combination with 5'-hydroxyl poly(A) or poly(C)
AgNO3
ammonium sulfate
beta,gamma-imidoadenosine 5'-triphosphate
-
binds with high affinity, similar to ATP
beta,gamma-imidoadenylyl 5'-tetraphosphate
-
ATP analog, competitive against ATP, noncompetitive against 5'-OH-DNA, serves as substrate for the reverse reaction only
Ca2+
-
inhibits in combination with MgCl2, stimulates without MgCl2
Cd2+
-
-
Chloramphenicol
Cibacron blue F3GA
-
chromophore of blue dextran, inhibition is competitive to single stranded DNA, noncompetitive with respect to ATP
CTP
-
more than 90% inhibition at 0.3 mM
dATP
-
more than 95% inhibition at 0.3 mM
dCTP
-
80% inhibition at 0.3 mM
Deoxyribonucleoside triphosphates
-
-
Dextran sulfate
-
dGTP
-
more than 95% inhibition at 0.3 mM
diphosphate
dTTP
-
more than 95% inhibition at 0.3 mM
GTP
-
more than 90% inhibition at 0.3 mM
heparin
iodoacetate
N-ethylmaleimide
-
-
Ni2+
-
inhibits in combination with MgCl2, stimulates without MgCl2
p-chloromercuribenzoate
p-hydroxymercuribenzoate
-
2-mercaptoethanol prevents inhibition
PEG 6000
-
5-15%, 3-4fold increase in activity, inhibitory above
phosphate
Ribonucleoside 3'-phosphates
-
weak
Ribonucleoside triphosphates
-
-
sodium hydrogen phosphate
-
-
-
spermine
-
1 mM enhances activity 3times, inhibition above 1 mM
sulfate
sulfhydryl antagonists
-
-
-
tert-butyl 2-(1-hydroxy-2,2-diphenylethyl)-6-methyl-5,7-dioxo-2,4a,5,6,7,7a-hexahydro-1H-pyrrolo[3,4-b]pyridine-1yl-carbamate
-
A26B11C2
UTP
-
more than 90% inhibition at 0.3 mM
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
bovine serum albumin
-
dithiothreitol
PEG 6000
-
5-15%, 3-4fold increase in activity, inhibitory above
Polyamines
-
Polyethylene glycol
-
4-10%, stimulates
spermidine
spermine
sulfhydryl reagents
XRCC1
-
XRCC4
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.099
5'-dephospho-GAAAA-RNA
pH and temperature not specified in the publication
-
0.109
5'-dephospho-GC-RNA
pH and temperature not specified in the publication
-
0.0028
5'-HO-CCGACCAACGAAGGT
-
wild type enzyme, at pH 7.0 and 37C
-
0.0025
5'-hydroxyl poly(A)
-
pH 8.4, 37C
0.0034
5'-hydroxyl poly(C)
-
pH 8.4, 37C
0.016
5'-OH DNA
-
0.0027 - 0.046
5'-OH-DNA
0.021
5'-phospho-DNA
-
0.2
ADP
-
dephosphorylation of single-stranded oligonucleotides, pH 7.6, 37C; phosphate exchange reaction between nucleotides, reverse reaction, pH 7.6, 37C
0.00069 - 3.4
ATP
0.00056
GGGCC(AG)10GGCCC-fluorescein
-
-
0.5 - 2.5
Mg2+
0.1
Mn2+
-
pH 6.0, 37C
0.008
oligo (dT)25
-
polymin P precipitable enzyme, pH 7.5, 37C
-
0.0222 - 0.143
oligonucleotides
-
depending on the 5'-base and the length of the oligonucleotide, pH 7.6, 37C
0.0036
Poly(A)
-
pH 8.4, 37C
0.0013 - 0.0015
r(A20)
-
0.22 - 3.1
[gamma-S]ATP
0.53
[gamma-S]GTP
-
pH 8.4, 37C
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.008 - 1.6
3'-CMP
2.6
5'-dephospho-GAAAA-RNA
Caenorhabditis elegans
P52874
pH and temperature not specified in the publication
-
2.9
5'-dephospho-GC-RNA
Caenorhabditis elegans
P52874
pH and temperature not specified in the publication
-
0.072
5'-HO-CCGACCAACGAAGGT
Ruminiclostridium thermocellum
-
wild type enzyme, at pH 7.0 and 37C
-
0.077
5'-OH DNA
Pyrococcus horikoshii
Q57936
-
0.00083
5'-phospho-DNA
Pyrococcus horikoshii
Q57936
-
0.00005 - 2.9
ATP
198
GGGCC(AG)10GGCCC-fluorescein
Enterobacteria phage T4
P06855
-
-
1.9 - 2.6
r(A20)
-
0.00283
[gamma-S]ATP
synthetic ribozyme
-
pH-independent, 30C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.8
ADP
synthetic ribozyme
-
pH-independent in the range pH 6.0-8.5, 30C
3 - 11
beta,gamma-imidoadenylyl 5'-tetraphosphate
0.2 - 5
diphosphate
0.2 - 7
sulfate
additional information
additional information
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00006
2-(1-hydroxyundecyl)-1-(4-nitrophenylamino)-6-phenyl-6,7a-dihydro-1H-pyrrolo[3,4-b]pyridine-5,7(2H,4aH)-dione
Homo sapiens
-
-
0.07
ADP
Enterobacteria phage T4
-
at pH 7.0 and 37C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0002
-
purified, polymin P precipitable enzyme, pH 5.5, 37C
0.0007
-
partially purified enzyme, substrate RNA
0.0012
-
purified enzyme
0.0028
-
purified enzyme
0.0043
-
purified enzyme
0.005
-
above, purified enzyme, 30C
0.006
-
partially purified enzyme
0.0167
-
purified enzyme
0.0418
-
purified enzyme
0.125
-
purified enzyme, substrate RNA
0.393
-
purified enzyme
0.53
-
purified enzyme
2.67
-
substrate r(A20), pH 6.0, 65C
3.67
-
substrate d(A20), pH 6.0, 65C
5.67
-
purified wild-type
7
-
purified mutant pseT 1
30 - 40
-
commercial preparation
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
reverse reaction
5.5 - 7.5
-
3-CMP kinase activit
6 - 9
-
broad optimum
6.2
-
imidazole buffer
7 - 9
-
polymin P precipitable enzyme
7.8
-
inhibition assay
7.9 - 8.9
-
-
8.4
-
assay at, substrate RNA
9
-
substrate RNA
additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4
-
50% of maximum activity
4.5 - 6.5
RNA kinase activity
4.5 - 9.5
DNA kinase activity
4.5 - 7
5 - 7
-
pH 5: about 5% of activity maximum, pH 7: about 30% of activity maximum
5 - 9.5
-
about 50% of activity maximum at pH 5.0 and pH 9.5
5 - 6.5
-
pH 5: about 50% of activity maximum, pH 6.5: about 35% of activity maximum
6.5 - 8.9
-
pH 6.5: about 50% of activity maximum, pH 7.9-8.9: activity maximum, substrate RNA
7.4 - 8
-
forward reaction, optimal range
7.5 - 9.4
-
pH 7.5: about 50% of activity maximum, pH 8.4 and pH 9.4: about 85% of activity maximum
7.5 - 10
-
more than 80% of maximum activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 30
-
-
additional information
synthetic ribozyme
-
detailed reaction kinetics, pH- and temperature-dependence
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0 - 37
-
0C: about 7% of activity maximum, 37C: activity maximum, bacteriophage T4 enzyme
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5
-
-
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
33200
-
4 * 33200, analytical ultracentrifugation
38000
-
gel filtration
39000
-
4 * 39000, recombinant protein with His10-tag, calculated, protein is either a stable but asymmetrically shaped homotetramer or a metastable tetramer that is prone to dissociate to a homodimer
41000
determined by SDS-PAGE, tag-free
48000
x * 48000, SDS-PAGE
54000
-
1 * 54000, SDS-PAGE
56000
-
gel filtration
57100
-
-
57102
-
1 * 58000, SDS-PAGE, 1 * 57102, calculated
58000
-
sedimentation equilibrium analysis
60000
-
x * 60000, SDS-PAGE
70000
-
gel filtration, sucrose density gradient centrifugation
72000
-
sucrose density gradient centrifugation
79000
-
gel filtration
80000 - 160000
93000
-
1 * 93000, SDS-PAGE
96000
-
gel filtration, native PAGE
140000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
monomer
tetramer
additional information