ExplorEnz: EC 6.5.1.6

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6.5.1.6

Accepted name:

DNA ligase (ATP or NAD⁺)

Reaction:

(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

Systematic name:

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

Comments:

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).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, MetaCyc, PDB

References:

1.	Rolland, J.L., Gueguen, Y., Persillon, C., Masson, J.M. and Dietrich, J. Characterization of a thermophilic DNA ligase from the archaeon Thermococcus fumicolans. FEMS Microbiol. Lett. 236 (2004) 267–273. [DOI] [PMID: 15251207]
2.	Kim, Y.J., Lee, H.S., Bae, S.S., Jeon, J.H., Yang, S.H., Lim, J.K., Kang, S.G., Kwon, S.T. and Lee, J.H. Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp. Biotechnol. Lett. 28 (2006) 401–407. [DOI] [PMID: 16614906]

[EC 6.5.1.6 created 2014, modified 2016]