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Literature summary for 6.5.1.2 extracted from

  • Lim, J.H.; Choi, J.; Han, S.J.; Kim, S.H.; Hwang, H.Z.; Jin, D.K.; Ahn, B.Y.; Han, Y.S.
    Molecular cloning and characterization of thermostable DNA ligase from Aquifex pyrophilus, a hyperthermophilic bacterium (2001), Extremophiles, 5, 161-168.
    View publication on PubMed

Activating Compound

Activating Compound Comment Organism Structure
KCl highest activity at 150 mM Aquifex pyrophilus
NaCl highest activity at 200 mM Aquifex pyrophilus
NH4Cl highest activity at 200 mM Aquifex pyrophilus
potassium glutamate highest activity at 350 mM Aquifex pyrophilus

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli Aquifex pyrophilus

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ 40% of activity obtained with Mg2+ Aquifex pyrophilus
Cu2+ 30% of activity obtained with Mg2+ Aquifex pyrophilus
K+ highest activity below 10 mM Thermus aquaticus
Mg2+ required Aquifex pyrophilus
Mn2+ 50% of activity obtained with Mg2+ Aquifex pyrophilus
Na+ inhibitory Thermus aquaticus
NH4+ highest activity below 10 mM Thermus aquaticus
Ni2+ 10% of activity obtained with Mg2+ Aquifex pyrophilus
Zn2+ 5% of activity obtained with Mg2+ Aquifex pyrophilus

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
82000
-
SDS-PAGE Aquifex pyrophilus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Thermus aquaticus DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Escherichia coli DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Aquifex pyrophilus DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?

Organism

Organism UniProt Comment Textmining
Aquifex pyrophilus Q9F150
-
-
Escherichia coli
-
-
-
Thermus aquaticus
-
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant protein Aquifex pyrophilus

Reaction

Reaction Comment Organism Reaction ID
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide 3 steps of reaction: 1. adenylation of the ligase in the presence of NAD+, 2. transferring the adenylate moiety to the 5'-phosphate of the nicked DNA substrate, 3. sealing the nick through the formation of a phosphodiester bond Thermus aquaticus
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide 3 steps of reaction: 1. adenylation of the ligase in the presence of NAD+, 2. transferring the adenylate moiety to the 5'-phosphate of the nicked DNA substrate, 3. sealing the nick through the formation of a phosphodiester bond Escherichia coli
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide 3 steps of reaction: 1. adenylation of the ligase in the presence of NAD+, 2. transferring the adenylate moiety to the 5'-phosphate of the nicked DNA substrate, 3. sealing the nick through the formation of a phosphodiester bond Aquifex pyrophilus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Thermus aquaticus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Aquifex pyrophilus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA Thermus aquaticus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA Aquifex pyrophilus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
-
Escherichia coli
50
-
-
Thermus aquaticus
65
-
above 65°C Aquifex pyrophilus

Temperature Range [°C]

Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
5 50
-
Escherichia coli
20 90
-
Thermus aquaticus
30 90
-
Aquifex pyrophilus

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
95
-
50% of activity lost within 15 min Thermus aquaticus
95
-
50% of activity lost within 5 min Escherichia coli
95
-
60 min, less than 25% of activity lost Aquifex pyrophilus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8 8.6
-
Aquifex pyrophilus

Cofactor

Cofactor Comment Organism Structure
NAD+ required Thermus aquaticus
NAD+ required Escherichia coli
NAD+ required Aquifex pyrophilus