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Literature summary for 6.5.1.1 extracted from

  • Engler, M.J.; Richardson, C.C.
    DNA ligases (1982), The Enzymes, 3rd Ed. (Boyer, P. D. , ed. ), 15, 3-29.
No PubMed abstract available

Activating Compound

Activating Compound Comment Organism Structure
Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required Mammalia
Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required eukaryota
Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required Tequatrovirus T4
Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required Escherichia phage T7

Application

Application Comment Organism
analysis essential reagent in studies on nucleic acid structure and metabolism. In combination with polynucleotide kinase end-group labeling, DNA ligase can be used to identify 3'- and 5'-end groups at single-strand interruptions by nearest neighbor analysis. DNA Mammalia
analysis essential reagent in studies on nucleic acid structure and metabolism. In combination with polynucleotide kinase end-group labeling, DNA ligase can be used to identify 3'- and 5'-end groups at single-strand interruptions by nearest neighbor analysis. DNA Tequatrovirus T4
analysis essential reagent in studies on nucleic acid structure and metabolism. In combination with polynucleotide kinase end-group labeling, DNA ligase can be used to identify 3'- and 5'-end groups at single-strand interruptions by nearest neighbor analysis. DNA Escherichia phage T7

Inhibitors

Inhibitors Comment Organism Structure
Cs+
-
Tequatrovirus T4
dATP
-
Escherichia phage T7
dATP
-
Mammalia
dATP competitive with respect to ATP Tequatrovirus T4
K+
-
Tequatrovirus T4
Li+
-
Tequatrovirus T4
Na+
-
Tequatrovirus T4
NH4+
-
Tequatrovirus T4
spermidine
-
Tequatrovirus T4
spermine
-
Tequatrovirus T4

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information
-
Mammalia
0.0000015
-
DNA internal phosphomonoesters in nicked natural DNA Tequatrovirus T4
0.0002 0.0015 ATP DNA ligase I Mammalia
0.0003
-
ATP ATP-diphosphate exchange reaction Escherichia phage T7
0.0006
-
DNA for either the joining of oligo(dT)10 on poly(dA) or the joining of DNA fragments with a two base-pair overhang generated by a restriction enzyme Tequatrovirus T4
0.004
-
dATP dATP-diphosphate exchange reaction Escherichia phage T7
0.006
-
ATP joinig reaction Escherichia phage T7
0.014
-
ATP joining reaction Tequatrovirus T4
0.045 0.1 ATP DNA ligase II Mammalia
0.05
-
DNA blunt end joining Tequatrovirus T4

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Mammalia
Mg2+ required Tequatrovirus T4
Mg2+ optimal concentration: 10 mM Tequatrovirus T4
Mn2+ 25% as effective as Mg2+ in activation Tequatrovirus T4

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
63000
-
1 * 63000, PAGE under denaturing and reducing conditions Tequatrovirus T4
68000
-
gel filtration Tequatrovirus T4
85000
-
gel filtration Mammalia
200000
-
gel filtration Mammalia

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Mammalia
-
?
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Saccharomyces cerevisiae
-
?
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Tequatrovirus T4 DNA ligase mutations drastically affect DNA synthesis, little effect on genetic recombination and repair of UV damage ?
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Escherichia phage T7 mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli ?
-
?

Organism

Organism UniProt Comment Textmining
Escherichia phage T7
-
-
-
eukaryota
-
-
-
Mammalia
-
-
-
Saccharomyces cerevisiae
-
-
-
Schizosaccharomyces pombe
-
-
-
Tequatrovirus T4
-
-
-

Purification (Commentary)

Purification (Comment) Organism
-
Tequatrovirus T4

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Mammalia AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
eukaryota AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Saccharomyces cerevisiae AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Schizosaccharomyces pombe AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m catalyzes blunt end joining of DNA Tequatrovirus T4 AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA ligase joins oligo(dT)*poly(A) Escherichia phage T7 AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m joins DNA annealed to RNA and, to a slight extent, even RNA annealed to its complementary RNA strand Tequatrovirus T4 AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Mammalia ?
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Saccharomyces cerevisiae ?
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA ligase mutations drastically affect DNA synthesis, little effect on genetic recombination and repair of UV damage Tequatrovirus T4 ?
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli Escherichia phage T7 ?
-
?
ATP + DNA
-
Tequatrovirus T4 AMP + diphosphate + ?
-
?
dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Mammalia dAMP + diphosphate + (deoxyribonucleotide)n+m
-
?
dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m at 0.5% of the activity relative to ATP Tequatrovirus T4 dAMP + diphosphate + (deoxyribonucleotide)n+m
-
?
dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m at 35-50% of the activity relative to ATP Escherichia phage T7 dAMP + diphosphate + (deoxyribonucleotide)n+m
-
?
additional information
-
Mammalia ?
-
?
additional information ATP-diphosphate exchange reaction Tequatrovirus T4 ?
-
?
additional information ATP-diphosphate exchange reaction Escherichia phage T7 ?
-
?

Subunits

Subunits Comment Organism
monomer
-
Mammalia
monomer
-
Saccharomyces cerevisiae
monomer
-
Escherichia phage T7
monomer 1 * 63000, PAGE under denaturing and reducing conditions Tequatrovirus T4

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
joining of the blunt ends of duplex structures 16 nucleotides or longer Tequatrovirus T4
25
-
blunt end ligation, 16mer or longer Tequatrovirus T4

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.2 7.8 joining of nicks in Tris-HCl buffer Tequatrovirus T4
7.2 7.7 in Tris-HCl buffer Escherichia phage T7
7.4 8 DNA ligase I, in Tris-HCl buffer Mammalia

pH Range

pH Minimum pH Maximum Comment Organism
6.9 8 6.9: 46% of maximal activity, 8.0: 65% of maximal activity Tequatrovirus T4
7.2 8.4 7.2-7.7: maximal activity, 8.4: 50% of maximal activity Escherichia phage T7