6.5.1.2: DNA ligase (NAD+)

This is an abbreviated version!
For detailed information about DNA ligase (NAD+), go to the full flat file.

Reaction

Synonyms

beta-NAD+ -dependent DNA ligase, beta-NAD+-dependent DNA ligase, Deoxyribonucleate ligase, Deoxyribonucleic acid joinase, Deoxyribonucleic acid ligase, Deoxyribonucleic joinase, Deoxyribonucleic ligase, Deoxyribonucleic repair enzyme, Deoxyribonucleic-joining enzyme, DNA joinase, DNA ligase, DNA ligase (NAD), DNA repair enzyme, DNA-joining enzyme, LigA, Ligase, polynucleotide (nicotinamide adenine dinucleotide), LigN, MimiLIG, MsEPV DNA ligase, MtuLigA, NAD(+)-dependent DNA ligase, NAD+ dependent DNA ligase, NAD+ DNA ligase, NAD+-dependent DNA ligase, NAD+-dependent DNA ligase A, NAD-dependent DNA ligase, NDL, Polydeoxyribonucleotide synthase (NAD+), Polydeoxyribonucleotide synthase [NAD+], Polynucleotide ligase, Polynucleotide synthetase, Polynucleotide synthetase (nicotinamide adenine dinucleotide), Rv3014c, Synthetase, polydeoxyribonucleotide (nicotinamide adenine dinucleotide), T4 DNA ligase, Taq DNA ligase, Tfi DNA ligase, Tth DNA ligase, wBm-LigA

ECTree

     6 Ligases

         6.5 Forming phosphoric-ester bonds

             6.5.1 Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)

                6.5.1.2 DNA ligase (NAD+)

Advanced search results

Do not include text mining results

Include results (more...)

Include results (more...)

Results	in table
16	Activating Compound
48846	AA Sequence
22	Application
1	CAS Registry Number
51	Cloned(Commentary)
120	Cofactor
13	Crystallization (Commentary)
1	Expression
3	General Information
1	General Stability
449	IC50 Value
614	Inhibitors
7	Ki Value [mM]
38	KM Value [mM]
85	Metals/Ions
27	Molecular Weight [Da]
112	Natural Substrates/ Products (Substrates)
877	Organism
56	PDB ID
20	pH Optimum
8	pH Range
1	pH Stability
183	Protein Variants
51	Purification (Commentary)
32	Reaction
1	Reaction Type
193	Reference
5	Specific Activity [micromol/min/mg]
5	Storage Stability
245	Substrates and Products (Substrate)
13	Subunits
249	Synonyms
1	Systematic Name
24	Temperature Optimum [°C]
10	Temperature Range [°C]
16	Temperature Stability [°C]
15	Turnover Number [1/s]

Reaction

print visible entries

print all entries

Reaction on EC 6.5.1.2 - DNA ligase (NAD+)

Please wait a moment until all data is loaded. This message will disappear when all data is loaded.

top print hide show all columns Go to Reaction Search

Please wait a moment until the data is sorted. This message will disappear when the data is sorted.

REACTION

REACTION DIAGRAM

COMMENTARY

ORGANISM

UNIPROT

LITERATURE

(deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP

(1c)

-

-

-

ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide

19 entries

NAD+ + [DNA ligase]-L-lysine = [DNA ligase]-N6-(5'-adenylyl)-L-lysine + beta-nicotinamide D-nucleotide

(1a)

-

-

-

[DNA ligase]-N6-(5'-adenylyl)-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine

(1b)

-

-

-

ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide

the second step is the transfer of the AMP moiety from the enzyme to the 5'-phosphoryl of the DNA substrate, recreating a diphosphate linkage and thereby preserving the high-energy bond. The third step is the nucleophilic attack of the adjacent 3'-hydroxyl group to form a phosphodiester bond and eliminate AMP

Escherichia coli

-

1974

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

Staphylococcus aureus

-

651683

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

Thermus aquaticus

-

651212

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

Bacillus subtilis

-

650937

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

Thermus thermophilus

-

1979

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

Escherichia coli

-

651073, 651212, 652360, 652463, 652489, 653376, 653388

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

Geobacillus stearothermophilus

-

652786, 653923

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

Thermus scotoductus

-

651073, 652489

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

Thermus filiformis

-

649250

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

-

650937

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

Melanoplus sanguinipes

-

650937

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 pyrophilus

-

649444

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

Amsacta moorei entomopoxvirus

-

650937, 652175

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 pyrophilus

Q9F150

651212

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

Thermus filiformis

Q9ZHI0

650967

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

O66880

653379

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

Pseudoalteromonas haloplanktis

Q9RBF2

651073

ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide

mechanism, the initial step is most likely a nucleophilic attack of the epsilon-amino group of a Lys on the adenylyl phosphorus of NAD+

Escherichia coli

-

1909, 1974

ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide

overall reaction

-

-

-