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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Escherichia phage T7 and UniProt Accession P00969

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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).
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Escherichia phage T7
UNIPROT: P00969
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Word Map
The taxonomic range for the selected organisms is: Escherichia phage T7
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
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
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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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-
-
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Deoxyribonucleic joinase
-
-
-
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Deoxyribonucleic ligase
-
-
-
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Deoxyribonucleic repair enzyme
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-
-
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Deoxyribonucleic-joining enzyme
-
-
-
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DNA joinase
-
-
-
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DNA ligase
-
-
-
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DNA ligase I
-
-
-
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DNA ligase II
-
-
-
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DNA ligase III
-
-
-
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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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Lig(Tk)
-
-
-
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Pfu DNA ligase
-
-
-
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Polydeoxyribonucleotide synthase (ATP)
-
-
-
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Polydeoxyribonucleotide synthase [ATP]
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-
-
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Polynucleotide ligase
-
-
-
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Sealase
-
-
-
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T4 ATP ligase
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-
SYSTEMATIC NAME
IUBMB Comments
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).
CAS REGISTRY NUMBER
COMMENTARY hide
9015-85-4
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
?
show the reaction diagram
-
mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
dAMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
-
at 35-50% of the activity relative to ATP
-
-
?
additional information
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
?
show the reaction diagram
-
mutants fail to produce progeny phage when grown on ligase-deficient strains of E. coli
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
AMPPNP
-
nonhydrolyzable ATP analogue
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Reducing agent
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reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0003 - 0.006
ATP
0.004
dATP
-
dATP-diphosphate exchange reaction
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2 - 7.7
-
in Tris-HCl buffer
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2 - 8.4
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7.2-7.7: maximal activity, 8.4: 50% of maximal activity
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DNLI_BPT7
359
0
41133
Swiss-Prot
other Location (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K159L
-
adenylation site mutant, aboragates the ability of the ligase to covalently link to an AMP moiety
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant domain 1, i.e. residues 1-240 and domain 2, i.e. residues 241-359
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of domain 1, i.e. residues 1-240 and domain 2, i.e. residues 241-359 in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
-
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Shuman, S.
Closing the gap on DNA ligase
Structure
4
653-656
1996
Escherichia phage T7
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Cao, W.
DNA ligases: Structure, function and mechanism
Curr. Org. Chem.
6
827-839
2002
Escherichia phage T7, Vaccinia virus, Chlorella virus
-
Manually annotated by BRENDA team
Doherty, A.J.; Wigley, D.B.
Functional domains of an ATP-dependent DNA ligase
J. Mol. Biol.
285
63-71
1999
Escherichia phage T7
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team