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EC Tree
IUBMB 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).
The taxonomic range for the selected organisms is: Geobacillus stearothermophilus The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
+
+
5'-phospho-(deoxyribonucleotide)m
=
+
+
beta-nicotinamide D-nucleotide
Synonyms
nad(+)-dependent dna ligase, taq dna ligase, nad+-dependent dna ligase, tfi dna ligase, nad-dependent dna ligase, tth dna ligase, mimilig, mtuliga, wbm-liga, polynucleotide synthetase,
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NAD+-dependent DNA ligase
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Deoxyribonucleate ligase
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Deoxyribonucleic acid joinase
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Deoxyribonucleic acid ligase
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Deoxyribonucleic joinase
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Deoxyribonucleic ligase
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Deoxyribonucleic repair enzyme
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Deoxyribonucleic-joining enzyme
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DNA repair enzyme
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DNA-joining enzyme
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Ligase, polynucleotide (nicotinamide adenine dinucleotide)
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Polydeoxyribonucleotide synthase (NAD+)
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Polydeoxyribonucleotide synthase [NAD+]
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Polynucleotide ligase
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Polynucleotide synthetase
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Polynucleotide synthetase (nicotinamide adenine dinucleotide)
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Synthetase, polydeoxyribonucleotide (nicotinamide adenine dinucleotide)
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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
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poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (NAD+)
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).
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NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA
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?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA
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?
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NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA
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?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA
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Zn2+
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bound to the C-terminal fragment
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UniProt
brenda
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DNLJ_GEOSE
670
0
74231
Swiss-Prot
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30000
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SDS-PAGE, C-terminal fragment
30040
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ESI-mass spectrometry, C-terminal fragment
35790
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ESI-mass spectrometry, N-terminal fragment
36000
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SDS-PAGE, N-terminal fragment
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hanging drop vapour phase diffusion method, K114A mutant protein fragment
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DELTA1-396
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no self adenylation activity, DNA-binding not affected
DELTA319-670
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full self adenylation activity but strongly reduced DNA-binding and ligation activity
K114A
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prevention of partial adenylation of the enzyme
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fragments overexpressed in Escherichia coli
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1-318 fragment with K114A mutation
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N-terminal fragment 1-318 and C-terminal fragment starting from position 397 seperately expressed in Escherichia coli BL21
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medicine
NAD+-dependent ligases can serve as a valuable target in the development of chemotherapeutics for the treatment of numerous human ailments
medicine
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potential target for antibiotics due to the fact that eukaryotic cells use ATP instead of NAD+ as cofactor for DNA-ligase
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Timson, D.J.; Wigley, D.B.
Functional domains of an NAD+-dependent DNA ligase
J. Mol. Biol.
285
73-83
1999
Geobacillus stearothermophilus
brenda
Singleton, M.R.; Hakansson, K.; Timson, D.J.; Wigley, D.B.
Structure of the adenylation domain of an NAD+-dependent DNA ligase
Structure
7
35-42
1999
Geobacillus stearothermophilus
brenda
Dwivedi, N.; Dube, D.; Pandey, J.; Singh, B.; Kukshal, V.; Ramachandran, R.; Tripathi, R.P.
NAD+-dependent DNA ligase: a novel target waiting for the right inhibitor
Med. Res. Rev.
28
545-568
2008
Escherichia coli, Geobacillus stearothermophilus (O87703), Mycobacterium tuberculosis (P9WNV1), Enterococcus faecalis (Q837V6), Thermus filiformis (Q9ZHI0), Mycobacterium tuberculosis H37Rv (P9WNV1)
brenda