EC Explorer

6.5.1.6

DNA ligase (ATP or NAD⁺)

(1) ATP + (deoxyribonucleotide)_n-3′-hydroxyl + 5′-phospho-(deoxyribonucleotide)_m = (deoxyribonucleotide)_n+m + AMP + diphosphate (overall reaction);;(1a) ATP + [DNA ligase]-L-lysine = 5′-adenosyl [DNA ligase]-N^ε-phosphono-L-lysine + diphosphate;;(1b) 5′-adenosyl [DNA ligase]-N^ε-phosphono-L-lysine + 5′-phospho-(deoxyribonucleotide)_m = 5′-(5′-diphosphoadenosine)-(deoxyribonucleotide)_m + [DNA ligase]-L-lysine;;(1c) (deoxyribonucleotide)_n-3′-hydroxyl + 5′-(5′-diphosphoadenosine)-(deoxyribonucleotide)_m = (deoxyribonucleotide)_n+m + AMP;;(2) NAD⁺ + (deoxyribonucleotide)_n-3′-hydroxyl + 5′-phospho-(deoxyribonucleotide)_m = (deoxyribonucleotide)_n+m + AMP + β-nicotinamide D-nucleotide (overall reaction);;(2a) NAD⁺ + [DNA ligase]-L-lysine = 5′-adenosyl [DNA ligase]-N^ε-phosphono-L-lysine + β-nicotinamide D-nucleotide;;(2b) 5′-adenosyl [DNA ligase]-N^ε-phosphono-L-lysine + 5′-phospho-(deoxyribonucleotide)_m = 5′-(5′-diphosphoadenosine)-(deoxyribonucleotide)_m + [DNA ligase]-L-lysine;;(2c) (deoxyribonucleotide)_n-3′-hydroxyl + 5′-(5′-diphosphoadenosine)-(deoxyribonucleotide)_m = (deoxyribonucleotide)_n+m + AMP

poly(deoxyribonucleotide)-3′-hydroxyl:5′-phospho-poly(deoxyribonucleotide) ligase (ATP or NAD⁺)

The enzymes from the archaea Thermococcus fumicolans and Thermococcus onnurineus show high activity with either ATP or NAD⁺, and significantly lower activity with TTP, GTP, and CTP. The enzyme catalyses the ligation of DNA strands with 3′-hydroxyl and 5′-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex DNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP or NAD⁺, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5′-phosphate terminus of the substrate, forming the capped structure 5′-(5′-diphosphoadenosine)-[DNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3′-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate. Different from EC 6.5.1.1, DNA ligase (ATP), EC 6.5.1.2, DNA ligase (NAD⁺) and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).

created 2014, modified 2016