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Information on EC 6.5.1.6 - DNA ligase (ATP or NAD+) and Organism(s) Thermococcus onnurineus and UniProt Accession B6YTR4

for references in articles please use BRENDA:EC6.5.1.6
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EC Tree
IUBMB 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).
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Thermococcus onnurineus
UNIPROT: B6YTR4
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The taxonomic range for the selected organisms is: Thermococcus onnurineus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
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Synonyms
tfu dna ligase, more
SYSTEMATIC NAME
IUBMB Comments
poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP or NAD+)
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).
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
show the reaction diagram
Q2Q452
about 10% of the activity compared to ATP
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
Q2Q452
the enzyme displays nick joining and blunt-end ligation activity. ATP and NAD+ are comparably active
-
-
?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
Q2Q452
about 20% of the activity compared to ATP
-
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)n+m
show the reaction diagram
Q2Q452
the enzyme displays nick joining and blunt-end ligation activity. ATP and NAD+ are comparably active
-
-
?
TTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
TMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
Q2Q452
about 20% of the activity compared to ATP
-
-
?
UTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
UMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
Q2Q452
about 15% of the activity compared to ATP
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
Q2Q452
1 mM, 2.5fold stimulation
Zn2+
Q2Q452
1 mM, 1.5 fold stimulation
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ca2+
Q2Q452
1 mM, about 25% loss of activity
Mn2+
Q2Q452
1 mM, about 50% loss of activity
Ni2+
Q2Q452
1 mM, about 70% loss of activity
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
Q2Q452
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9
Q2Q452
pH 7.0: about 60% of maximal activity, pH 9.0: about 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
65 - 90
Q2Q452
65°C: about 50% of maximal activity, 90°C: about 95% of maximal activity
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
63000
Q2Q452
x * 63000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
Q2Q452
x * 63000, SDS-PAGE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kim, Y.J.; Lee, H.S.; Bae, S.S.; Jeon, J.H.; Yang, S.H.; Lim, J.K.; Kang, S.G.; Kwon, S.T.; Lee, J.H.
Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp.
Biotechnol. Lett.
28
401-407
2006
Thermococcus onnurineus (Q2Q452)
Manually annotated by BRENDA team