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Literature summary for 6.5.1.2 extracted from
- DNA and RNA ligases (EC 6.5.1.1, EC 6.5.1.2, and EC 6.5.1.3) (1993), Methods Mol. Biol., 16, 213-230.
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| additional information | no requirement for sulfhydryl reagent | Escherichia coli |
Application
| Application | Comment | Organism |
|---|---|---|
| synthesis | DNA ligase is used for cDNA cloning by replacement synthesis | Escherichia coli |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
- |
Escherichia coli |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| Mn2+ | activation at 0.2-1.0 mM, inhibition at higher concentration | Escherichia coli |  |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.000025 | 0.00056 | 5'-phosphate terminus of deoxyribonucleotides | - |
Salmonella enterica subsp. enterica serovar Typhimurium | |
| 0.000025 | 0.00056 | 5'-phosphate terminus of deoxyribonucleotides | - |
Bacillus subtilis | |
| 0.000025 | 0.00056 | 5'-phosphate terminus of deoxyribonucleotides | - |
Thermus thermophilus | |
| 0.000025 | 0.00056 | 5'-phosphate terminus of deoxyribonucleotides | - |
Escherichia coli | |
| 0.00003 | 0.00007 | NAD+ | - |
Salmonella enterica subsp. enterica serovar Typhimurium | |
| 0.00003 | 0.00007 | NAD+ | - |
Bacillus subtilis | |
| 0.00003 | 0.00007 | NAD+ | - |
Thermus thermophilus | |
| 0.00003 | 0.00007 | NAD+ | - |
Escherichia coli | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Ca2+ | 60% as active as Mg2+ in activation as reported in one study, no activity in another | Escherichia coli | |
| K+ | - |
Thermus thermophilus | |
| K+ | stimulates | Escherichia coli | |
| Mg2+ | requires divalent cations, Mn2+ or Mg2+ | Thermus thermophilus | |
| Mg2+ | requires divalent cations, Mn2+ or Mg2+ | Escherichia coli | |
| Mg2+ | optimal concentration: 1-3 mM | Escherichia coli | |
| Mn2+ | requires divalent cations, Mn2+ or Mg2+ | Thermus thermophilus | |
| Mn2+ | requires divalent cations, Mn2+ or Mg2+ | Escherichia coli | |
| Mn2+ | activation at 0.2-1.0 mM, inhibition at higher concentration | Escherichia coli | |
| NH4+ | - |
Thermus thermophilus | |
| NH4+ | stimulates | Escherichia coli | |
| Rb+ | stimulates | Escherichia coli | |
| Zn2+ | slight activation | Escherichia coli | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 74000 | - |
1 * 74000, SDS-PAGE of denatured and reduced enzyme | Escherichia coli |
| 77000 | - |
sedimentation equilibrium ultracentrifugation | Escherichia coli |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Salmonella enterica subsp. enterica serovar Typhimurium | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | ? | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Bacillus subtilis | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | ? | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Thermus thermophilus | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | ? | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Escherichia coli | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | - |
- |
- |
| Escherichia coli | - |
- |
- |
| Salmonella enterica subsp. enterica serovar Typhimurium | - |
- |
- |
| Thermus thermophilus | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + 5'-phosphate terminus of deoxyribonucleotides | - |
Salmonella enterica subsp. enterica serovar Typhimurium | ? | - |
? | |
| ATP + 5'-phosphate terminus of deoxyribonucleotides | - |
Bacillus subtilis | ? | - |
? | |
| ATP + 5'-phosphate terminus of deoxyribonucleotides | - |
Thermus thermophilus | ? | - |
? | |
| ATP + 5'-phosphate terminus of deoxyribonucleotides | - |
Escherichia coli | ? | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase requires two DNA termini, the 5'-terminus, carrying a phosphate group, and the 3'-terminus, a hydroxyl group. These termini must reside on a double-stranded molecule, DNA:DNA or DNA:RNA. Both strands of the duplex may terminate, in the form of a staggered end or a blunt end, and the ligase then requires a second similar double-stranded terminus to join the two in an intermolecular reaction. Alternatively, the two termini may be provided by a nick in just one strand of a duplex, which the enzyme will then seal | Salmonella enterica subsp. enterica serovar Typhimurium | AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase requires two DNA termini, the 5'-terminus, carrying a phosphate group, and the 3'-terminus, a hydroxyl group. These termini must reside on a double-stranded molecule, DNA:DNA or DNA:RNA. Both strands of the duplex may terminate, in the form of a staggered end or a blunt end, and the ligase then requires a second similar double-stranded terminus to join the two in an intermolecular reaction. Alternatively, the two termini may be provided by a nick in just one strand of a duplex, which the enzyme will then seal | Bacillus subtilis | AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase requires two DNA termini, the 5'-terminus, carrying a phosphate group, and the 3'-terminus, a hydroxyl group. These termini must reside on a double-stranded molecule, DNA:DNA or DNA:RNA. Both strands of the duplex may terminate, in the form of a staggered end or a blunt end, and the ligase then requires a second similar double-stranded terminus to join the two in an intermolecular reaction. Alternatively, the two termini may be provided by a nick in just one strand of a duplex, which the enzyme will then seal | Thermus thermophilus | AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase requires two DNA termini, the 5'-terminus, carrying a phosphate group, and the 3'-terminus, a hydroxyl group. These termini must reside on a double-stranded molecule, DNA:DNA or DNA:RNA. Both strands of the duplex may terminate, in the form of a staggered end or a blunt end, and the ligase then requires a second similar double-stranded terminus to join the two in an intermolecular reaction. Alternatively, the two termini may be provided by a nick in just one strand of a duplex, which the enzyme will then seal | Escherichia coli | AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | no ligation of blunt-ended or flush-ended DNAs | Escherichia coli | AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | Salmonella enterica subsp. enterica serovar Typhimurium | ? | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | Bacillus subtilis | ? | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | Thermus thermophilus | ? | - |
? | |
| NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m | joining of short DNA fragments formed during DNA replication and so enabling DNA synthesis to progress in an overall 3'-5' direction on the antiparallel strand of the double helix, while continual 5'-3' synthesis proceeds on the other strand. Plays a role during genetic recombination and in the repair of UV-damaged DNA | Escherichia coli | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| monomer | - |
Thermus thermophilus |
| monomer | 1 * 74000, SDS-PAGE of denatured and reduced enzyme | Escherichia coli |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 10 | 15 | ligation of cohesive ends | Escherichia coli |
| 24 | 37 | cohesive-end DNA restriction fragments | Thermus thermophilus |
| 65 | 72 | nick-closing activity | Thermus thermophilus |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.5 | 8 | Tris-HCl buffer | Escherichia coli |
| 8 | - |
- |
Thermus thermophilus |
| 8 | - |
sodium phosphate buffer | Escherichia coli |
pH Range
| pH Minimum | pH Maximum | Comment | Organism |
|---|---|---|---|
| 5.6 | 7.5 | 50% of maximal activity at pH 5.6 and 7.5, potassium phosphate buffer | Escherichia coli |
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