Information on EC 6.5.1.7 - DNA ligase (ATP, ADP or GTP)

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
6.5.1.7
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RECOMMENDED NAME
GeneOntology No.
DNA ligase (ATP, ADP or GTP)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
show the reaction diagram
(1c); catalytic reaction mechanism, detailed overview
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(deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP
show the reaction diagram
(3c)
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5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
show the reaction diagram
(1b); (2b)
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5'-guanosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
show the reaction diagram
(3b)
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ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate
show the reaction diagram
ADP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + phosphat
show the reaction diagram
(2a)
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ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate
show the reaction diagram
ATP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + diphosphate
show the reaction diagram
(1a)
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GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP + diphosphate
show the reaction diagram
GTP + [DNA ligase]-L-lysine = 5'-guanosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + diphosphate
show the reaction diagram
(3a)
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SYSTEMATIC NAME
IUBMB Comments
poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP, ADP or GTP)
The enzymes from the archaea Hyperthermus butylicus and Sulfophobococcus zilligii are active with ATP, ADP or GTP. They show no activity with NAD+. 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, ADP, or GTP, forming a phosphoramide bond between adenylate/guanylate and a lysine residue. The nucleotide is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine/guanosine)-[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 nucleotide. Different from EC 6.5.1.1, DNA ligase (ATP), and EC 6.5.1.6, DNA ligase (ATP or NAD+), which cannot utilize GTP.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
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in Tris-HCl buffer
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 8
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pH 5.0: about 75% of maximal activity, pH 8.0: about 55% of maximal activity
6.5 - 9
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pH 6.5: about 90% of maximal activity, 9.0: about 95% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60 - 80
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60°C: about 55% of maximal activity, 80°C: about 60% of maximal activity
65 - 90
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65°C: about 40% of maximal activity, 90°C: about 40% of maximal activity
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
68000
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x * 68000, SDS-PAGE
70000
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x * 70000, enzyme with His-tag, SDS-PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystals are obtained by the microbatch crystallization method at 22°C, 2.9 A resolution using synchrotron radiation. The crystals belong to space group P1, with unit-cell parameters a = 63.7 A, b = 77.1 A, c = 77.8 A, alpha = 83.4°, beta = 82.4°, gamma = 74.6°
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
75
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the enzyme reaches its maximum activity when incubated at 75°C for 1 h and gradually loses its activity thereafter
94
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2.3 h, about 50% loss of activity
95
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half-life: 2.6 h
99
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half-life: 1.7 h
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed under control of the T7lac promoter of pTARG in Escherichia coli BL21-Codon-Plus(DE3)-RIL
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expression in Escherichia coli with a hexahistidine tag at the C-terminus
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