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EC Tree
IUBMB Comments 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, 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 6.5.1.2, DNA ligase (NAD+), 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: Escherichia phage T7 The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
+
+
5'-phospho-(deoxyribonucleotide)m
=
+
+
Synonyms
dna ligase, dna repair enzyme, dna ligase i, t4 dna ligase, dna ligase iv, dna ligase iii, ligase 1, dna ligase ii, polynucleotide ligase, dna ligase 1,
more
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ATP-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 acid repair enzyme
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Deoxyribonucleic acid-joining enzyme
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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 ligase IV homolog
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DNA repair enzyme
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DNA-joining enzyme
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Polydeoxyribonucleotide synthase (ATP)
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Polydeoxyribonucleotide synthase [ATP]
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Polynucleotide ligase
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poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP)
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, 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 6.5.1.2, DNA ligase (NAD+), 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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ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
?
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mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli
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-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
dAMP + diphosphate + (deoxyribonucleotide)n+m
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at 35-50% of the activity relative to ATP
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?
additional information
?
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ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
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both nick sealing and blunt end ligation
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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active on single-stranded RNA
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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can ligate nicked, cohesive, and blunt-ended DNA fragments
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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DNA ligase joins oligo(dT)*poly(A)
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?
additional information
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the ATP-dependent DNA ligase from bacteriophage T7 is a two-domain ligase: the adenylation or nucleotide-binding domain binds ATP and is connected to an OB-fold domain by a flexible linker. The ATP-binding pocket within the amino-terminal domain of bacteriophage T7 is formed by two antiparallel beta-sheets flanked by R-helices
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additional information
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ATP-diphosphate exchange reaction
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additional information
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ATP-diphosphate exchange reaction
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additional information
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ATP-diphosphate exchange reaction
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ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
?
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mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli
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-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
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-
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
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?
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AMPPNP
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nonhydrolyzable ATP analogue
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Reducing agent
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reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required
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0.004
dATP
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dATP-diphosphate exchange reaction
0.0003
ATP
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ATP-diphosphate exchange reaction
0.006
ATP
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joinig reaction
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7.2 - 7.7
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in Tris-HCl buffer
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7.2 - 8.4
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7.2-7.7: maximal activity, 8.4: 50% of maximal activity
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Uniprot
brenda
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DNLI_BPT7
359
0
41133
Swiss-Prot
other Location (Reliability: 2 )
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41000
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41000
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equilibrium sedimentation
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monomer
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monomer
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1 * 41000, SDS-PAGE
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K159L
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adenylation site mutant, aboragates the ability of the ligase to covalently link to an AMP moiety
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recombinant domain 1, i.e. residues 1-240 and domain 2, i.e. residues 241-359
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expression of domain 1, i.e. residues 1-240 and domain 2, i.e. residues 241-359 in Escherichia coli
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analysis
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essential reagent in studies on nucleic acid structure and metabolism. In combination with polynucleotide kinase end-group labeling, DNA ligase can be used to identify 3'- and 5'-end groups at single-strand interruptions by nearest neighbor analysis. DNA
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Engler, M.J.; Richardson, C.C.
DNA ligases
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
15
3-29
1982
Tequatrovirus T4, Escherichia phage T7, Saccharomyces cerevisiae, eukaryota, Mammalia, Schizosaccharomyces pombe
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brenda
Maunders, M.J.
DNA and RNA ligases (EC 6.5.1.1, EC 6.5.1.2, and EC 6.5.1.3)
Methods Mol. Biol.
16
213-230
1993
Tequatrovirus T4, Escherichia phage T7, Mammalia
brenda
Subramanya, H.S.; Doherty, A.J.; Ashford, S.R.; Wigley, D.B.
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7
Cell
85
607-615
1996
Escherichia phage T7
brenda
Shuman, S.
Closing the gap on DNA ligase
Structure
4
653-656
1996
Escherichia phage T7
brenda
Doherty, A.J.; Ashford, S.R.; Subramanya, H.S.; Wigley, D.B.
Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization
J. Biol. Chem.
271
11083-11089
1996
Tequatrovirus T4, Escherichia phage T7
brenda
Montecuccho, A.; Pedrali-Noy, G.; Spadari, S.; Lestingi, M.; Ciarrocchi, G.
Effects of DNA-binding drugs on T4 DNA ligase
Biochem. J.
266
379-384
1990
Escherichia phage T7
brenda
Cao, W.
DNA ligases: Structure, function and mechanism
Curr. Org. Chem.
6
827-839
2002
Escherichia phage T7, Vaccinia virus, Chlorella virus
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brenda
Doherty, A.J.; Wigley, D.B.
Functional domains of an ATP-dependent DNA ligase
J. Mol. Biol.
285
63-71
1999
Escherichia phage T7
brenda
Tomkinson, A.E.; Vijayakumar, S.; Pascal, J.M.; Ellenberger, T.
DNA ligases: Structure, reaction mechanism, and function
Chem. Rev.
106
687-699
2006
Escherichia phage T7 (P00969), Homo sapiens (P18858)
brenda