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Literature summary for 6.5.1.2 extracted from

  • Tong, J.; Barany, F.; Cao, W.
    Ligation reaction specificities of an NAD+-dependent DNA ligase from the hyperthermophile Aquifex aeolicus (2000), Nucleic Acids Res., 28, 1447-1454.
    View publication on PubMedView publication on EuropePMC

Activating Compound

Activating Compound Comment Organism Structure
KCl 150 mM Aquifex aeolicus

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli Aquifex aeolicus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.00008
-
nicked DNA pH 7.6, 65°C Aquifex aeolicus

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ supports formation of DNA-adenylate intermediate Aquifex aeolicus
Mg2+ 5 mM Aquifex aeolicus
Mn2+ 5 mM, most effective metal cofactor Aquifex aeolicus
Ni2+ supports formation of DNA-adenylate intermediate Aquifex aeolicus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Aquifex aeolicus 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 aeolicus O66880
-
-

Purification (Commentary)

Purification (Comment) Organism
-
Aquifex aeolicus

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 Aquifex aeolicus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + nicked DNA
-
Aquifex aeolicus AMP + diphosphate + ?
-
?
ATP + nicked DNA
-
Aquifex aeolicus ?
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m activity depends on the base pairs on both sides of the nick, T/A Aquifex aeolicus 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 aeolicus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.033
-
nicked DNA pH 7.6, 65°C Aquifex aeolicus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
-
Aquifex aeolicus

Cofactor

Cofactor Comment Organism Structure
NAD+ required, highest activity at 0.5 mM Aquifex aeolicus