BRENDA - Enzyme Database show
show all sequences of 2.7.1.78

Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkp-hen1 RNA repair system

Das, U.; Wang, L.K.; Smith, P.; Shuman, S.; Biochemistry 52, 4734-4743 (2013)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expressed in Escherichia coli BL21(DE3) cells
Hungateiclostridium thermocellum
Crystallization (Commentary)
Crystallization
Organism
in complexes with GTP, CTP, UTP and dATP, hanging drop vapor diffusion method, using 100 mM sodium citrate, pH 5.6, 100 mM MgCl2, 16-18% (w/v) PEG-3350
Hungateiclostridium thermocellum
Engineering
Amino acid exchange
Commentary
Organism
R116A
the mutation elicits a 10fold increase in Km for ATP, but has little effect on the turnover number value leading to 83% of wild type activity
Hungateiclostridium thermocellum
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.0028
-
5'-HO-CCGACCAACGAAGGT
wild type enzyme, at pH 7.0 and 37°C
Hungateiclostridium thermocellum
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Hungateiclostridium thermocellum
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ATP + 5'-dephospho-DNA
Hungateiclostridium thermocellum
-
ADP + 5'-phospho-DNA
-
-
r
ATP + 5'-dephospho-RNA
Hungateiclostridium thermocellum
-
ADP + 5'-phospho-RNA
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Hungateiclostridium thermocellum
A3DJ38
-
-
Purification (Commentary)
Commentary
Organism
Ni-agarose column chromatography, and gel filtration
Hungateiclostridium thermocellum
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ADP + 5'-HO-AUCACGCUUpCp
-
737681
Hungateiclostridium thermocellum
?
-
-
-
r
ATP + 5'-dephospho-DNA
-
737681
Hungateiclostridium thermocellum
ADP + 5'-phospho-DNA
-
-
-
r
ATP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
ADP + 5'-phospho-RNA
-
-
-
r
ATP + 5'-HO-CCGACCAACGAAGGT
-
737681
Hungateiclostridium thermocellum
?
-
-
-
r
CTP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
CDP + 5'-phospho-RNA
-
-
-
r
dATP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
dADP + 5'-phospho-RNA
-
-
-
r
GTP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
GDP + 5'-phospho-RNA
-
-
-
r
UTP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
UDP + 5'-phospho-RNA
-
-
-
r
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.072
-
5'-HO-CCGACCAACGAAGGT
wild type enzyme, at pH 7.0 and 37°C
Hungateiclostridium thermocellum
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli BL21(DE3) cells
Hungateiclostridium thermocellum
Crystallization (Commentary) (protein specific)
Crystallization
Organism
in complexes with GTP, CTP, UTP and dATP, hanging drop vapor diffusion method, using 100 mM sodium citrate, pH 5.6, 100 mM MgCl2, 16-18% (w/v) PEG-3350
Hungateiclostridium thermocellum
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
R116A
the mutation elicits a 10fold increase in Km for ATP, but has little effect on the turnover number value leading to 83% of wild type activity
Hungateiclostridium thermocellum
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.0028
-
5'-HO-CCGACCAACGAAGGT
wild type enzyme, at pH 7.0 and 37°C
Hungateiclostridium thermocellum
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Hungateiclostridium thermocellum
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ATP + 5'-dephospho-DNA
Hungateiclostridium thermocellum
-
ADP + 5'-phospho-DNA
-
-
r
ATP + 5'-dephospho-RNA
Hungateiclostridium thermocellum
-
ADP + 5'-phospho-RNA
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
Ni-agarose column chromatography, and gel filtration
Hungateiclostridium thermocellum
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ADP + 5'-HO-AUCACGCUUpCp
-
737681
Hungateiclostridium thermocellum
?
-
-
-
r
ATP + 5'-dephospho-DNA
-
737681
Hungateiclostridium thermocellum
ADP + 5'-phospho-DNA
-
-
-
r
ATP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
ADP + 5'-phospho-RNA
-
-
-
r
ATP + 5'-HO-CCGACCAACGAAGGT
-
737681
Hungateiclostridium thermocellum
?
-
-
-
r
CTP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
CDP + 5'-phospho-RNA
-
-
-
r
dATP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
dADP + 5'-phospho-RNA
-
-
-
r
GTP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
GDP + 5'-phospho-RNA
-
-
-
r
UTP + 5'-dephospho-RNA
-
737681
Hungateiclostridium thermocellum
UDP + 5'-phospho-RNA
-
-
-
r
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.072
-
5'-HO-CCGACCAACGAAGGT
wild type enzyme, at pH 7.0 and 37°C
Hungateiclostridium thermocellum
Other publictions for EC 2.7.1.78
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
751515
Zhang
Determination of the activity ...
Escherichia virus T4
Microchim. Acta
186
003
2019
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
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-
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1
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-
749573
Ma
-
A fluorescence-based assay fo ...
Escherichia virus T4
Anal. Methods
8
1989-1994
2016
-
1
-
-
-
-
1
-
-
-
-
-
-
1
-
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1
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1
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1
1
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
737436
Tao
Highly specific fluorescence d ...
Escherichia virus T4
Anal. Biochem.
485
18-24
2015
-
-
-
-
-
-
3
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
2
-
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-
-
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3
-
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-
1
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-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
737444
Zhou
One-strand oligonucleotide pro ...
Escherichia virus T4
Analyst
140
5650-5655
2015
-
-
-
-
-
-
3
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
737890
Lian
Detection of T4 polynucleotide ...
Escherichia virus T4
Biosens. Bioelectron.
66
316-320
2015
-
-
-
-
-
-
3
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
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-
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-
-
-
-
3
-
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-
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-
1
-
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-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
750414
Shimada
Polynucleotide kinase-phospha ...
Mus musculus
EMBO J.
34
2465-2480
2015
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
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-
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-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
751906
Chatterjee
The role of the mammalian DNA ...
Homo sapiens
PLoS Genet.
11
e1004749
2015
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
2
-
-
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-
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-
-
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-
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-
-
1
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-
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-
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-
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-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
752288
Dong
A label-free assay for T4 pol ...
Escherichia virus T4
Talanta
146
253-258
2015
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
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-
-
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-
-
-
-
-
-
1
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-
-
-
-
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
729562
Karaca
Human CLP1 mutations alter tRN ...
Homo sapiens
Cell
157
636-650
2014
-
-
-
-
2
-
-
-
-
-
-
1
-
1
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
729563
Schaffer
CLP1 founder mutation links tR ...
Homo sapiens
Cell
157
651-663
2014
-
-
-
-
1
-
-
-
-
-
1
1
-
3
-
-
-
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
737441
Hou
Amplified detection of T4 poly ...
Escherichia virus T4
Anal. Chem.
86
884-890
2014
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
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-
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-
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-
1
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-
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-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
737443
Wang
Detection of polynucleotide ki ...
Escherichia virus T4
Analyst
139
3895-3900
2014
-
-
-
-
-
-
3
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
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3
-
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1
-
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2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
737575
Strazdaite-Zieliene
A mutation in the gene for pol ...
Escherichia virus T4, Escherichia virus T4 K10
Arch. Virol.
159
327-331
2014
-
-
1
-
2
-
-
-
-
-
-
6
-
3
-
-
1
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
2
-
-
-
-
-
-
-
-
6
-
-
-
1
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
738535
Das
Structures of bacterial polynu ...
Hungateiclostridium thermocellum, Hungateiclostridium thermocellum DSM 1237
J. Bacteriol.
196
4285-4292
2014
-
-
1
1
4
-
-
-
-
1
-
2
-
3
-
-
1
-
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
4
-
-
-
-
-
-
1
-
2
-
-
-
1
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
739067
Dikfidan
RNA specificity and regulation ...
Caenorhabditis elegans
Mol. Cell
54
975-986
2014
-
-
1
1
-
-
-
3
-
-
-
-
-
2
-
-
-
-
-
-
-
-
3
-
-
-
-
3
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
3
-
-
-
-
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-
-
-
-
-
-
3
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
729174
Mair
Intron excision from precursor ...
Homo sapiens
Biochem. Soc. Trans.
41
831-837
2013
-
-
-
-
1
-
-
-
-
-
-
2
-
1
-
-
-
-
-
1
-
-
2
-
-
-
-
-
-
-
-
-
-
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-
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-
-
1
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-
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-
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-
-
2
-
-
-
-
-
1
-
-
2
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
730493
Das
Mechanism of RNA 2,3-cyclic ph ...
Escherichia virus T4
Nucleic Acids Res.
41
355-365
2013
-
-
1
-
-
-
-
-
-
-
-
1
-
1
-
-
1
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
1
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
737431
Ma
Simultaneous detection of kina ...
Escherichia virus T4
Anal. Biochem.
443
166-168
2013
-
-
-
-
-
-
-
-
-
-
-
2
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
737681
Das
Structural and biochemical ana ...
Hungateiclostridium thermocellum
Biochemistry
52
4734-4743
2013
-
-
1
1
1
-
-
1
-
1
-
2
-
2
-
-
1
-
-
-
-
-
8
-
-
-
-
1
-
-
-
-
-
-
-
-
-
1
-
1
1
-
-
-
-
1
-
1
-
2
-
-
-
1
-
-
-
-
8
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
737888
Zhang
Double strand DNA-templated co ...
Escherichia virus T4
Biosens. Bioelectron.
44
6-9
2013
-
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Recognition of DNA substrates ...
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Mani
Spectroscopic studies of DNA a ...
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Biochemistry
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Mutational analysis defines th ...
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Polynucleotide kinase. A versa ...
Escherichia virus T4, Mammalia
Structure
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Fanta
Production, characterization, ...
Homo sapiens
Hybridoma
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642004
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Polynucleotide kinase (EC 2.7. ...
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Purification and kinetic prope ...
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642015
Pheiffer
Deoxyribonucleic acid kinase f ...
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Shuman
5-Hydroxyl polyribonucleotide ...
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Nichols
A rapid purification of T4 pol ...
Escherichia virus T4
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Lillehaug
Inhibition of T4 polynucleotid ...
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Austin
Purification and properties of ...
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Lillehaug
Physicochemical properties of ...
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642009
Lillehaug
Phosphorylation of double-stra ...
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Biochemistry
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Levin
A deoxyribonucleic acid kinase ...
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Teraoka
Polynucleotide kinase from rat ...
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642008
Panet
Physical characterization and ...
Escherichia virus T4
Biochemistry
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5045-5050
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Novogrodsky
The enzymatic phosphorylation ...
Enterobacteria phage T2, Escherichia virus T4, no activity in bacteriophage T1, no activity in bacteriophage T5
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Novogrodsky
The enzymatic phosphorylation ...
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