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Literature summary 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

EC Number Activating Compound Comment Organism Structure
6.5.1.1 Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required Mammalia
6.5.1.1 Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required eukaryota
6.5.1.1 Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required Tequatrovirus T4
6.5.1.1 Reducing agent reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required Escherichia phage T7
6.5.1.2 additional information no requirement for sulfhydryl reagent Escherichia coli

Application

EC Number Application Comment Organism
6.5.1.1 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
6.5.1.1 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
6.5.1.1 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
6.5.1.2 analysis DNA ligase is an essential reagent in studies on nucleic acid structure and metabolism Escherichia coli
6.5.1.2 analysis DNA ligase, in combination with polynucleotide kinase, can be used to identify 3'- and 5'-end groups at single-strand interruptions by nearest neighbor analysis Escherichia coli
6.5.1.2 analysis DNA ligase can be used to determine the ability of other enzymes to act at nicks and gaps in duplex DNA molecules Escherichia coli
6.5.1.2 analysis DNA ligase can be used to study the primary and secondary structure of DNA molecules Escherichia coli
6.5.1.2 synthesis DNA ligase is an indispensible reagent in the chemical synthesis of double-stranded DNA of specific nucleotide sequence Escherichia coli
6.5.1.2 synthesis an important use of DNA ligase is the preparation of recombinant DNA molecules for use in the cloning of DNA Escherichia coli

Cloned(Commentary)

EC Number Cloned (Comment) Organism
6.5.1.2
-
 Escherichia coli

Inhibitors

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

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
6.5.1.1 additional information
-
 additional information
-
 Mammalia
6.5.1.1 0.0000015
-
 DNA internal phosphomonoesters in nicked natural DNA Tequatrovirus T4
6.5.1.1 0.0002 0.0015 ATP DNA ligase I Mammalia
6.5.1.1 0.0003
-
 ATP ATP-diphosphate exchange reaction Escherichia phage T7
6.5.1.1 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
6.5.1.1 0.004
-
 dATP dATP-diphosphate exchange reaction Escherichia phage T7
6.5.1.1 0.006
-
 ATP joinig reaction Escherichia phage T7
6.5.1.1 0.014
-
 ATP joining reaction Tequatrovirus T4
6.5.1.1 0.045 0.1 ATP DNA ligase II Mammalia
6.5.1.1 0.05
-
 DNA blunt end joining Tequatrovirus T4

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
6.5.1.1 Mg2+ required Mammalia
6.5.1.1 Mg2+ required Tequatrovirus T4
6.5.1.1 Mg2+ optimal concentration: 10 mM Tequatrovirus T4
6.5.1.1 Mn2+ 25% as effective as Mg2+ in activation Tequatrovirus T4
6.5.1.2 Ca2+ 60% as active as Mg2+ in activation as reported in one study, no activity in another Escherichia coli
6.5.1.2 K+ stimulates at low concentrations Escherichia coli
6.5.1.2 Mg2+ requires divalent cations, Mn2+ or Mg2+ Escherichia coli
6.5.1.2 Mg2+ optimal concentration: 1-3 mM Escherichia coli
6.5.1.2 Mn2+ requires divalent cations, Mn2+ or Mg2+ Escherichia coli
6.5.1.2 NH4+ stimulates at low concentrations Escherichia coli
6.5.1.2 Zn2+ slight activation Escherichia coli

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
6.5.1.1 63000
-
 1 * 63000, PAGE under denaturing and reducing conditions Tequatrovirus T4
6.5.1.1 68000
-
 gel filtration Tequatrovirus T4
6.5.1.1 85000
-
 gel filtration Mammalia
6.5.1.1 200000
-
 gel filtration Mammalia

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Mammalia
-
 ?
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Saccharomyces cerevisiae
-
 ?
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Tequatrovirus T4 DNA ligase mutations drastically affect DNA synthesis, little effect on genetic recombination and repair of UV damage ?
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m Escherichia phage T7 mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli ?
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Salmonella enterica subsp. enterica serovar Typhimurium
-
 ?
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Bacillus subtilis
-
 ?
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Escherichia coli the enzyme is indispensable for normal cell growth and inviability of mutants seems to be primarily the result of an inability to seal Okazaki fragments ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
6.5.1.1 Escherichia phage T7
-
-
-
6.5.1.1 eukaryota
-
-
-
6.5.1.1 Mammalia
-
-
-
6.5.1.1 Saccharomyces cerevisiae
-
-
-
6.5.1.1 Schizosaccharomyces pombe
-
-
-
6.5.1.1 Tequatrovirus T4
-
-
-
6.5.1.2 Bacillus subtilis
-
-
-
6.5.1.2 Escherichia coli
-
-
-
6.5.1.2 Salmonella enterica subsp. enterica serovar Typhimurium
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
6.5.1.1
-
 Tequatrovirus T4

Reaction

EC Number Reaction Comment Organism Reaction ID
6.5.1.2 ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide mechanism, the initial step is most likely a nucleophilic attack of the epsilon-amino group of a Lys on the adenylyl phosphorus of NAD+ Escherichia coli
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Mammalia AMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 eukaryota AMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Saccharomyces cerevisiae AMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Schizosaccharomyces pombe AMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m catalyzes blunt end joining of DNA Tequatrovirus T4 AMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA ligase joins oligo(dT)*poly(A) Escherichia phage T7 AMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 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
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Mammalia ?
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Saccharomyces cerevisiae ?
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA ligase mutations drastically affect DNA synthesis, little effect on genetic recombination and repair of UV damage Tequatrovirus T4 ?
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli Escherichia phage T7 ?
-
 ?
6.5.1.1 ATP + DNA
-
 Tequatrovirus T4 AMP + diphosphate + ?
-
 ?
6.5.1.1 dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Mammalia dAMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m at 0.5% of the activity relative to ATP Tequatrovirus T4 dAMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m at 35-50% of the activity relative to ATP Escherichia phage T7 dAMP + diphosphate + (deoxyribonucleotide)n+m
-
 ?
6.5.1.1 additional information
-
 Mammalia ?
-
 ?
6.5.1.1 additional information ATP-diphosphate exchange reaction Tequatrovirus T4 ?
-
 ?
6.5.1.1 additional information ATP-diphosphate exchange reaction Escherichia phage T7 ?
-
 ?
6.5.1.2 additional information NAD+/nicotinamide nucleotide exchange reaction Escherichia coli ?
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Salmonella enterica subsp. enterica serovar Typhimurium AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Bacillus subtilis AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m oligonucleotides as short as six or seven in length can be joined if annealed to long complementary deoxyribonucleotides Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m joining of 5'-phosphoryl terminus of DNA chain to the 3'-hydroxyl terminus of RNA Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m the self-complementary polymer, poly(dA-dT), forms a looped-back structure that DNA ligase can join to yield a circular molecule Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m catalyzes the joining of polynucleotide strands provided they have juxtaposed 3'-hydroxyl and 5'-phosphoryl end groups aligned in a duplex structure: e.g. annealed ends of lamdda DNA, endogenous nicks in T5 DNA, interruptions created by the action of pancreatic DNAse, annealed fragments generated by the staggered cutting action of some restriction endonucleases Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Salmonella enterica subsp. enterica serovar Typhimurium ?
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Bacillus subtilis ?
-
 ?
6.5.1.2 NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m the enzyme is indispensable for normal cell growth and inviability of mutants seems to be primarily the result of an inability to seal Okazaki fragments Escherichia coli ?
-
 ?
6.5.1.2 NADH + (deoxyribonucleotide)n + (deoxyribonucleotide)m NADH has a significantly higher Km as NAD+ Escherichia coli ?
-
 ?
6.5.1.2 Thionicotinamide derivative of NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m significantly higher Km as NAD+ Escherichia coli ?
-
 ?

Subunits

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

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
6.5.1.1 25
-
 joining of the blunt ends of duplex structures 16 nucleotides or longer Tequatrovirus T4
6.5.1.1 25
-
 blunt end ligation, 16mer or longer Tequatrovirus T4

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.5.1.1 7.2 7.8 joining of nicks in Tris-HCl buffer Tequatrovirus T4
6.5.1.1 7.2 7.7 in Tris-HCl buffer Escherichia phage T7
6.5.1.1 7.4 8 DNA ligase I, in Tris-HCl buffer Mammalia
6.5.1.2 6.5
-
 NAD+/nicotinamide nucleotide exchange reaction Escherichia coli
6.5.1.2 7.5 8 Tris-HCl buffer Escherichia coli
6.5.1.2 8
-
 sodium phosphate buffer Escherichia coli

pH Range

EC Number pH Minimum pH Maximum Comment Organism
6.5.1.1 6.9 8 6.9: 46% of maximal activity, 8.0: 65% of maximal activity Tequatrovirus T4
6.5.1.1 7.2 8.4 7.2-7.7: maximal activity, 8.4: 50% of maximal activity Escherichia phage T7