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Literature summary for 6.5.1.1 extracted from
- Mammalian DNA ligases (1992), Annu. Rev. Biochem., 61, 251-281.
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| bovine serum albumin | stimulates | Mammalia | |
| additional information | human fibroblast line GM1492, but not several related fibroblast lines, expresses substantial amounts of a heat-stable protease-sensitive factor, which stimulates calf thymus DNA ligase I | Mammalia | |
| phosphate | DNA ligase I is a phosphoprotein, dephosphorylation causes drastic reduction in enzyme activity | Mammalia |  |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
- |
Drosophila melanogaster |
- |
Saccharomyces cerevisiae |
- |
Schizosaccharomyces pombe |
| amino acid sequence of human DNA ligase I and enzyme from Schizosaccharomyces pombe are virtually identical in the region of the active site, although the two enzymes show only 44% overall identity. The sequence of DNA ligase II appears to be quite different from that of DNA ligase I | Homo sapiens |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| R771W | Arg771-Trp mutation in DNA ligase I of cell line 46BR defective in DNA ligase I accounts for the malfunctioning but partly active enzyme present in 46BR cells that allows cell proliferation | Homo sapiens |
General Stability
| General Stability | Organism |
|---|---|
| DNA ligase I is highly sensitive to partial proteolysis | Mammalia |
| Tween 20, 0.2% or bovine serum albumin stabilizes | Mammalia |
| very susceptible to proteolysis | Drosophila melanogaster |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| Arabinosyl-2-fluoro-ATP | - |
Mammalia | |
| additional information | dephosphorylation causes drastic reduction in enzyme activity | Mammalia | |
| additional information | - |
Rattus norvegicus | |
| additional information | - |
Vaccinia virus | |
| pyridoxal 5'-phosphate | DNA ligase I | Mammalia | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0005 | 0.001 | ATP | DNA ligase I | Mammalia | |
| 0.0016 | - |
ATP | - |
Drosophila melanogaster | |
| 0.0016 | - |
ATP | - |
Homo sapiens | |
| 0.01 | 0.1 | ATP | DNA ligase II | Mammalia | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| nucleus | - |
Drosophila melanogaster | 5634 | - |
| nucleus | - |
Homo sapiens | 5634 | - |
| nucleus | - |
Bos taurus | 5634 | - |
| nucleus | DNA ligase I, II and III. DNA ligase I is more firmly associated with the nucleus than DNA ligase I. DNA ligase III is associated with the condensed chromatin that is present from anaphase to telophase | Mammalia | 5634 | - |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Mammalia | |
| Mg2+ | required | Homo sapiens | |
| Mg2+ | required | Rattus norvegicus | |
| Mg2+ | required | Bos taurus | |
| Mg2+ | required | Tequatrovirus T4 | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| additional information | - |
DNA ligase I, and II have a markedly asymetric structure, gel filtration data lead to a gross overestimation of the MW | Mammalia |
| 46000 | - |
1 * 46000 + 1 * 100000, DNA ligase III, SDS-PAGE. It cannot be concluded whether the 46000 MW peptide is an essential and integral part of DNA ligase III, or if it represents a separate protein that binds tentaciously to the 100000 MW DNA ligase component | Mammalia |
| 61000 | - |
enzyme-adenylate complex | Vaccinia virus |
| 100000 | - |
1 * 46000 + 1 * 100000, DNA ligase III, SDS-PAGE. It cannot be concluded whether the 46000 MW peptide is an essential and integral part of DNA ligase III, or if it represents a separate protein that binds tentaciously to the 100000 MW DNA ligase component | Mammalia |
| 102000 | - |
sucrose density gradient centrifugation | Mammalia |
| 160000 | - |
- |
Ambystoma mexicanum |
| 180000 | - |
- |
Xenopus laevis |
| 180000 | - |
- |
Pleurodeles sp. |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Drosophila melanogaster | - |
? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Homo sapiens | - |
? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Saccharomyces cerevisiae | - |
? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Bos taurus | - |
? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Tequatrovirus T4 | - |
? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Vaccinia virus | nonessential for viral DNA replication and growth on several types of host cells. DNA ligase I participates in DNA base excision repair as a component of a multiprotein complex | ? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | Mammalia | DNA ligase I is the key enzyme for joining Okazaki fragments during lagging-strand DNA synthesis in mammalian cells and also for completion of DNA excision repair processes | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Ambystoma mexicanum | - |
axolotl | - |
| Bos taurus | - |
calf | - |
| Bos taurus | - |
DNA ligase I, II | - |
| Drosophila melanogaster | - |
DNA ligase I and II | - |
| Homo sapiens | - |
DNA ligase I | - |
| Mammalia | - |
DNA ligase I, II, and III | - |
| Pleurodeles sp. | - |
- |
- |
| Rattus norvegicus | - |
- |
- |
| Saccharomyces cerevisiae | - |
- |
- |
| Schizosaccharomyces pombe | - |
- |
- |
| Tequatrovirus T4 | - |
- |
- |
| Vaccinia virus | - |
- |
- |
| Xenopus laevis | - |
- |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
- |
Bos taurus |
- |
Pleurodeles sp. |
- |
Ambystoma mexicanum |
| DNA ligase I, DNA ligase II partial | Drosophila melanogaster |
| DNA ligase II | Drosophila melanogaster |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate | mechanism: 1. formation of a covalent enzyme-adenylate complex, the ATP is cleaved to AMP and diphosphate with adenylyl residue linked by a phosphoramidate bond to the epsilon-amino group of a specific lysine residue at the active site of the protein, 2. the activated AMP residue of the DNA ligase-adenylate intermediate is transferred to the 5'-phosphate terminus of a single strand break in double-stranded DNA to generate a covalent DNA-AMP complex with a 5'-5' phosphoanhydride bond, 3. in the final step of DNA ligation, unadenylated DNA ligase is required for the generation of a phosphodiester bond and catalyzes displacement of the AMP residue through attack by adjacent 3'-hydroxyl group of the adenylylated site | Mammalia |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| egg | 10fold lower activity in adult tissues than in eggs | Xenopus laevis | - |
| egg | unfertilized, high activity of DNA ligase | Drosophila melanogaster | - |
| egg | unfertilized, high activity of DNA ligase | Xenopus laevis | - |
| egg | unfertilized, high activity of DNA ligase | Pleurodeles sp. | - |
| egg | unfertilized, high activity of DNA ligase | Ambystoma mexicanum | - |
| embryo | - |
Drosophila melanogaster | - |
| embryo | - |
Xenopus laevis | - |
| liver | - |
Rattus norvegicus | - |
| lymphoblast | - |
Mammalia | - |
| additional information | DNA ligase I correlates well with changes in DNA replication during development, the level of DNA ligase II activity does not change significantly between different developmental stages | Drosophila melanogaster | - |
| oocyte | - |
Xenopus laevis | - |
| thymus | - |
Bos taurus | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase I: performs blunt end ligation of DNA in presence of glycol, can ligate (rA)*poly(dT) hybrid substrate, unable to join oligo(rA)*poly(rU), unable to join oligo(dT)*poly(rA) | Drosophila melanogaster | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Drosophila melanogaster | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Mammalia | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Homo sapiens | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Rattus norvegicus | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Saccharomyces cerevisiae | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Bos taurus | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Xenopus laevis | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Schizosaccharomyces pombe | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Tequatrovirus T4 | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Pleurodeles sp. | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Ambystoma mexicanum | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates | Vaccinia virus | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | catalyzes blunt end ligation of DNA, cannot join an oligo(dT)*poly(rA) hybrid substrate | Xenopus laevis | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | joins restriction enzyme DNA fragments with staggered ends. Catalyzes blunt end ligation of DNA, this reaction is stimulated greatly by macromolecular crowding conditions. DNA ligase I is much more effective in blunt end joining than DNA ligase II and III, but is less efficient than T4 DNA ligase. DNA ligase acts at low efficiency as a topoisomerase, relaxing supercoiled DNA in an AMP-dependent reversal of the last step of the ligation reaction, joins oligo(dT) molecules hydrogen-bonded to poly(dA), is not able to ligate oligo(dT) with a poly(rA) complementary strand, can join oligo(rA) molecules hydrogen-bonded to poly(dT) | Mammalia | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | ligation of strand interruptions in oligo(dT)*poly(dA) | Vaccinia virus | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | ligates oligo(dT) with a poly(rA) complementary strand | Tequatrovirus T4 | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase I: seals single-strand breaks in DNA | Mammalia | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase II: can catalyze joining of an oligo(dT)*poly(rA) | Drosophila melanogaster | AMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | - |
Drosophila melanogaster | ? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | - |
Homo sapiens | ? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | - |
Saccharomyces cerevisiae | ? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | - |
Bos taurus | ? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | - |
Tequatrovirus T4 | ? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | nonessential for viral DNA replication and growth on several types of host cells. DNA ligase I participates in DNA base excision repair as a component of a multiprotein complex | Vaccinia virus | ? | - |
? | |
| ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | DNA ligase I is the key enzyme for joining Okazaki fragments during lagging-strand DNA synthesis in mammalian cells and also for completion of DNA excision repair processes | Mammalia | ? | - |
? | |
| dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | - |
Mammalia | dAMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m | - |
Tequatrovirus T4 | dAMP + diphosphate + (deoxyribonucleotide)n+m | - |
? | |
| additional information | DNA ligase I is induced upon cell proliferation, DNA ligase II, and III not | Mammalia | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| ? | - |
Homo sapiens |
| ? | - |
Saccharomyces cerevisiae |
| ? | - |
Bos taurus |
| ? | - |
Schizosaccharomyces pombe |
| ? | x * 83000-86000, SDS-PAGE | Drosophila melanogaster |
| dimer | 1 * 46000 + 1 * 100000, DNA ligase III, SDS-PAGE. It cannot be concluded whether the 46000 MW peptide is an essential and integral part of DNA ligase III, or if it represents a separate protein that binds tentaciously to the 100000 MW DNA ligase component | Mammalia |
| monomer | - |
Drosophila melanogaster |
| monomer | - |
Saccharomyces cerevisiae |
| monomer | - |
Bos taurus |
| monomer | - |
Tequatrovirus T4 |
| monomer | 1 * 68000-72000, DNA ligase II, SDS-PAGE | Mammalia |
| monomer | 1 * 125000-130000, DNA ligase I, SDS-PAGE | Mammalia |
Temperature Stability [°C]
| Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 42 | - |
- |
Bos taurus |
| 42 | - |
rapid inactivation, DNA ligase II | Mammalia |
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