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Literature summary for 6.5.1.2 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
Search for more literature for 6.5.1.2

Activating Compound

Activating Compound Comment Organism Structure
additional information no requirement for sulfhydryl reagent Escherichia coli

Application

Application Comment Organism
analysis DNA ligase is an essential reagent in studies on nucleic acid structure and metabolism Escherichia coli
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
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
analysis DNA ligase can be used to study the primary and secondary structure of DNA molecules Escherichia coli
synthesis DNA ligase is an indispensible reagent in the chemical synthesis of double-stranded DNA of specific nucleotide sequence Escherichia coli
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)

Cloned (Comment) Organism
-
 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+ stimulates at low concentrations Escherichia coli
Mg2+ requires divalent cations, Mn2+ or Mg2+ Escherichia coli
Mg2+ optimal concentration: 1-3 mM Escherichia coli
Mn2+ requires divalent cations, Mn2+ or Mg2+ Escherichia coli
NH4+ stimulates at low concentrations Escherichia coli
Zn2+ slight activation 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
-
 ?
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Bacillus subtilis
-
 ?
-
 ?
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

Organism UniProt Comment Textmining
Bacillus subtilis
-
-
-
Escherichia coli
-
-
-
Salmonella enterica subsp. enterica serovar Typhimurium
-
-
-

Reaction

Reaction Comment Organism Reaction ID
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)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information NAD+/nicotinamide nucleotide exchange reaction Escherichia coli ?
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Salmonella enterica subsp. enterica serovar Typhimurium AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Bacillus subtilis AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
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
-
 ?
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
-
 ?
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
-
 ?
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
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Salmonella enterica subsp. enterica serovar Typhimurium ?
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Bacillus subtilis ?
-
 ?
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 ?
-
 ?
NADH + (deoxyribonucleotide)n + (deoxyribonucleotide)m NADH has a significantly higher Km as NAD+ Escherichia coli ?
-
 ?
Thionicotinamide derivative of NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m significantly higher Km as NAD+ Escherichia coli ?
-
 ?

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
6.5
-
 NAD+/nicotinamide nucleotide exchange reaction Escherichia coli
7.5 8 Tris-HCl buffer Escherichia coli
8
-
 sodium phosphate buffer Escherichia coli