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Literature summary for 6.5.1.2 extracted from

  • Georlette, D.; Jonsson, Z.O.; Van Petegem, F.; Chessa, J.P.; Van Beeumen, J.; Hubscher, U.; Gerday, C.
    A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures (2000), Eur. J. Biochem., 267, 3502-3512.
    View publication on PubMed
Search for more literature for 6.5.1.2

Activating Compound

Activating Compound Comment Organism Structure
bovine serum albumin 0.025 mg/ml, stimulating Pseudoalteromonas haloplanktis
dithiothreitol 10 mM, stimulating Pseudoalteromonas haloplanktis

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli Pseudoalteromonas haloplanktis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.00017
-
 nicked DNA 4°C, pH 7.8 Pseudoalteromonas haloplanktis
0.00018
-
 nicked DNA 18°C, pH 7.8 Escherichia coli
0.00024
-
 nicked DNA 45°C, pH 7.8 Thermus scotoductus
0.0003
-
 nicked DNA 18°C, pH 7.8 Pseudoalteromonas haloplanktis
0.00047
-
 nicked DNA 60°C, pH 7.8 Thermus scotoductus
0.00063
-
 nicked DNA 25°C, pH 7.8 Pseudoalteromonas haloplanktis
0.0007
-
 nicked DNA 30°C, pH 7.8 Escherichia coli
0.00204
-
 nicked DNA 45°C, pH 7.8 Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
K+ 25 mM, stimulates activity Pseudoalteromonas haloplanktis
Mg2+ required Pseudoalteromonas haloplanktis
NH4+ 10 mM, stimulates activity Pseudoalteromonas haloplanktis
Zn2+ 0.24 mol per mol protein Pseudoalteromonas haloplanktis

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
74260
-
 Q-TOF-MS-mass spectrometry, non-adenylated form Pseudoalteromonas haloplanktis
74590
-
 Q-TOF-mass spectrometry, adenylated form Pseudoalteromonas haloplanktis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Escherichia coli DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Thermus scotoductus DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Pseudoalteromonas haloplanktis DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
-
-
Pseudoalteromonas haloplanktis Q9RBF2
-
-
Thermus scotoductus
-
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant enzyme from Escherichia coli Pseudoalteromonas haloplanktis

Reaction

Reaction Comment Organism Reaction ID
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
a
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
a
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
a

Storage Stability

Storage Stability Organism
-20°C, 20 mM Tris/HCl, pH 7.1, 50 mM NaCl, 0.1 mM EDTA, 50% glycerol Pseudoalteromonas haloplanktis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + nicked DNA
-
 Escherichia coli AMP + diphosphate + ?
-
 ?
ATP + nicked DNA
-
 Thermus scotoductus AMP + diphosphate + ?
-
 ?
ATP + nicked DNA
-
 Pseudoalteromonas haloplanktis AMP + diphosphate + ?
-
 ?
ATP + nicked DNA
-
 Escherichia coli ?
-
 ?
ATP + nicked DNA
-
 Thermus scotoductus ?
-
 ?
ATP + nicked DNA
-
 Pseudoalteromonas haloplanktis ?
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Thermus scotoductus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Pseudoalteromonas haloplanktis AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA Escherichia coli AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA Thermus scotoductus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA Pseudoalteromonas haloplanktis AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.01
-
 nicked DNA 4°C, pH 7.8 Pseudoalteromonas haloplanktis
0.016
-
 nicked DNA 45°C, pH 7.8 Escherichia coli
0.021
-
 nicked DNA 18°C, pH 7.8 Escherichia coli
0.03
-
 nicked DNA 30°C, pH 7.8 Escherichia coli
0.034
-
 nicked DNA 18°C, pH 7.8 Pseudoalteromonas haloplanktis
0.047
-
 nicked DNA 25°C, pH 7.8 Pseudoalteromonas haloplanktis
0.053
-
 nicked DNA 45°C, pH 7.8 Thermus scotoductus
0.132
-
 nicked DNA 60°C, pH 7.8 Thermus scotoductus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8.6
-
-
 Pseudoalteromonas haloplanktis

pH Range

pH Minimum pH Maximum Comment Organism
7.5 10.5 very low activity above or below this range Pseudoalteromonas haloplanktis

Cofactor

Cofactor Comment Organism Structure
NAD+ required Escherichia coli
NAD+ required Thermus scotoductus
NAD+ required Pseudoalteromonas haloplanktis