Reaction: NAD+ + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + β-nicotinamide D-nucleotide (overall reaction)
(1a) NAD+ + [DNA ligase]-L-lysine = [DNA ligase]-N6-(5'-adenylyl)-L-lysine + β-nicotinamide D-nucleotide
(1b) [DNA ligase]-N6-(5'-adenylyl)-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
Other name(s): polydeoxyribonucleotide synthase (NAD+); polynucleotide ligase (NAD+); DNA repair enzyme (ambiguous); DNA joinase (ambiguous); polynucleotide synthetase (nicotinamide adenine dinucleotide); deoxyribonucleic-joining enzyme (ambiguous); deoxyribonucleic ligase (ambiguous); deoxyribonucleic repair enzyme (ambiguous); deoxyribonucleic joinase (ambiguous); DNA ligase (ambiguous); deoxyribonucleate ligase (ambiguous); polynucleotide ligase (ambiguous); deoxyribonucleic acid ligase (ambiguous); polynucleotide synthetase (ambiguous); deoxyribonucleic acid joinase (ambiguous); DNA-joining enzyme (ambiguous); polynucleotide ligase (nicotinamide adenine dinucleotide); poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)
Systematic name: poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (NAD+)
Comments: The enzyme, typically found in bacteria, 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 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. RNA can also act as substrate, to some extent. cf. EC 6.5.1.1, DNA ligase (ATP), EC 6.5.1.6, DNA ligase (ATP or NAD+), and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37259-52-2
References:
1. Zimmerman, S.B., Little, J.W., Oshinsky, C.K. and Gellert, M. Enzymatic joining of DNA strands: a novel reaction of diphosphopyridine nucleotide. Proc. Natl. Acad. Sci. USA 57 (1967) 1841-1848. [PMID: 4291949]
2. Little, J.W., Zimmerman, S.B., Oshinsky, C.K. and Gellert, M. Enzymatic joining of DNA strands, II. An enzyme-adenylate intermediate in the dpn-dependent DNA ligase reaction. Proc. Natl. Acad. Sci. USA 58 (1967) 2004-2011. [PMID: 4295585]
3. Modorich, P. and Lehman, I.R. Deoxyribonucleic acid ligase. A steady state kinetic analysis of the reaction catalyzed by the enzyme from Escherichia coli. J. Biol. Chem. 248 (1973) 7502-7511. [PMID: 4355585]
4. Modrich, P., Anraku, Y. and Lehman, I.R. Deoxyribonucleic acid ligase. Isolation and physical characterization of the homogeneous enzyme from Escherichia coli. J. Biol. Chem. 248 (1973) 7495-7501. [PMID: 4355584]
5. Uphoff, S., Reyes-Lamothe, R., Garza de Leon, F., Sherratt, D.J. and Kapanidis, A.N. Single-molecule DNA repair in live bacteria. Proc. Natl. Acad. Sci. USA 110 (2013) 8063-8068. [PMID: 23630273]