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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Drosophila melanogaster
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6.5.1.1 DNA ligase (ATP)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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Word Map
- 6.5.1.1
- strand
- endonuclease
- nick
-
single-stranded
- ligases
- glycosylase
-
end-joining
-
nonhomologous
- duplex
- mismatch
- polymerases
-
phosphodiester
- dna-pkcs
-
polyadp-ribose
-
topoisomerase
- parp
- 8-oxoguanine
- temozolomide
-
dna-dependent
-
o6-methylguanine-dna
-
rejoin
- uracil
-
abasic
-
okazaki
-
blunt-ended
-
artemis
- fen1
- o6-methylguanine
- primase
-
o6-alkylguanine-dna
-
cross-complementing
-
tyrosyl-dna
-
overhang
-
apurinic
-
alkyltransferase
-
5'-phosphorylated
-
photolyase
-
uracil-dna
-
8-oxog
- mre11
-
mispaired
-
excises
- analysis
-
formamidopyrimidine-dna
- molecular biology
- 7,8-dihydro-8-oxoguanine
- o6-benzylguanine
- formamidopyrimidine
-
o6-alkylguanine
-
base-excision
- synthesis
-
klenow
- smurf1
The taxonomic range for the selected organisms is: Drosophila melanogaster
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
+
+
=
+
+
+
+
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
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Deoxyribonucleate ligase
-
-
-
-
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
-
-
-
-
Deoxyribonucleic ligase
-
-
-
-
Deoxyribonucleic repair enzyme
-
-
-
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Deoxyribonucleic-joining enzyme
-
-
-
-
DNA joinase
-
-
-
-
DNA ligase
-
-
-
-
DNA ligase I
-
-
-
-
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
-
-
-
-
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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-
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Sealase
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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
9015-85-4
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-O-(3-Thio)adenosine triphosphate + (deoxyribonucleotide)n + (deoxyribonucleotide)m
5'-O-(3-Thio)adenosine monophosphate + diphosphate + (deoxyribonucleotide)n+m
-
-
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
?
-
DNA ligase is biologically active to endonucleolytically cleaved pBR322 DNA
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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
-
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
-
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
DNA ligase I: performs blunt end ligation of DNA in presence of glycol, can ligate (rA)*poly(dT) hybrid substrate, unable to join oligo(rA)*poly(rU), unable to join oligo(dT)*poly(rA)
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
DNA ligase III: repairs single-strand breaks in DNA, but is unable to perform either blunt end ligation or AMP-dependent relaxation of supercoiled DNA. The enzyme can join both the oligo(dT)*poly(rA) and oligo(rA)*poly(dT) hybrid substrates
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
overview: activity of DNA ligase on ribo- and deoxyribopolymer substrates
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
reverse reaction: incubation of superhelical closed circular DNA molecules with the enzyme and AMP results in the production of a population of DNA molecules which have lost most of their superhelical density
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
DNA ligase I and II ligate 5'-phosphoryl and 3'-hydroxyl groups in oligo(dT) in the presence of poly(dA). DNA ligase II can join oligo(dT)*poly(rA)
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
p(dT)7U can be joined when annealed with poly(dA), joining of oligonucleotides containing a single mismatched nucleotide at their 3'-hydroxyl termini, as well as DNA containing short, complementary 5'-protruding ends, and in the presence of glycol 6000, blunt-ended duplex DNA
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
in addition to joining DNA to DNA the enzyme can join the 5'-phosphoryl terminus of RNA to the 3'-hydroxyl terminus of DNA or RNA, when they are annealed with DNA
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
can join a 3'-hydroxyl terminus of DNA to a 5'-hydroxyl terminus of RNA, can join oligo(rA)12*poly(dT), blunt end joining in presence of polyethylene glycol
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
inability to ligate oligo(dT)*poly(rA)
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
DNA ligase II: can catalyze joining of an oligo(dT)*poly(rA)
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
-
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
?
-
DNA ligase is biologically active to endonucleolytically cleaved pBR322 DNA
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
DNA ligase I is active at low salt concentrations, 0-30 mM KCl, DNA ligase II is active at high salt concentrations, 50-100 mM KCl
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dithiothreitol
-
required for optimal activity of DNA ligase I, but not for DNA ligase II activity
polyvinyl alcohol
-
required for optimal activity of DNA ligase I but not for DNA ligase II activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
-
DNA ligase I correlates well with changes in DNA replication during development, the level of DNA ligase II activity does not change significantly between different developmental stages
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). DNLI1_DROME
747
0
84719
Swiss-Prot
other Location (Reliability: 3)
Q9VYA5_DROME
918
0
104832
TrEMBL
other Location (Reliability: 1)
Q8MZC0_DROME
696
0
78085
TrEMBL
other Location (Reliability: 1)
Q9VG84_DROME
806
0
90848
TrEMBL
Mitochondrion (Reliability: 4)
Q8MS06_DROME
918
0
104774
TrEMBL
other Location (Reliability: 1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lindahl, T.; Barnes, D.E.
Mammalian DNA ligases
Annu. Rev. Biochem.
61
251-281
1992
Ambystoma mexicanum, Tequatrovirus T4, Bos taurus, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Mammalia, Pleurodeles sp., Rattus norvegicus, Schizosaccharomyces pombe, Vaccinia virus, Xenopus laevis
Tomkinson, A.E.; Levin, D.S.
Mammalian DNA ligases
BioEssays
19
893-901
1997
Bos taurus, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Mammalia, Schizosaccharomyces pombe, Vaccinia virus, Xenopus laevis
Lasko, D.D.; Tomkinson, A.E.; Lindahl, T.
Eukaryotic DNA ligases
Mutat. Res.
236
277-287
1990
Bos taurus, Saccharomyces cerevisiae, Drosophila melanogaster, Mammalia, Schizosaccharomyces pombe, Vaccinia virus
Rabin, B.A.; Chase, J.W.
DNA ligase from Drosophila melanogaster embryos. Substrate specificity and mechanism of action
J. Biol. Chem.
262
14105-14111
1987
Drosophila melanogaster
Rabin, B.A.; Hawley, R.S.; Chase, J.W.
DNA ligase from Drosophila melanogaster embryos. Purification and physical characterization
J. Biol. Chem.
261
10637-10645
1986
Drosophila melanogaster
Takahashi, M.; Tomizawa, K.
Purification and characterization of DNA ligase II from Drosophila melanogaster
Eur. J. Biochem.
192
735-740
1990
Drosophila melanogaster
Takahashi, M.; Senshu, M.
Two distinct DNA ligases from Drosophila melanogaster embryos
FEBS Lett.
213
345-352
1987
Drosophila melanogaster
Yutin, N.; Koonin, E.V.
Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity
Biol. Direct
4
51
2009
Acanthocystis turfacea chlorella virus 1, Acidobacterium capsulatum ATCC 51196, African swine fever virus, Agrotis segetum granulovirus, Aquifex aeolicus VF5, Arabidopsis thaliana, Archaeoglobus fulgidus DSM 4304, Chthoniobacter flavus, Chthoniobacter flavus Ellin428, Cinqassovirus aeh1, deerpox virus W-848-83, Dictyostelium discoideum, Drosophila melanogaster, Emiliania huxleyi virus 86, Entamoeba histolytica HM-1:IMSS, Enterobacteria phage, Erwinia phage, Escherichia phage V5, Fowlpox virus, Gemmata obscuriglobus UQM 2246, goatpox virus Pellor, Heliothis zea nudivirus, Homo sapiens, Lessievirus bcepil02, Lymantria dispar multiple nucleopolyhedrovirus, Marseillevirus, Methanosarcina acetivorans C2A, Methylibium petroleiphilum PM1, Monosiga brevicollis MX1, myxoma virus, Nanoarchaeum equitans Kin4-M, Nitrosopumilus maritimus SCM1, Okubovirus SPO1, Opitutus terrae PB90-1, Orgyia leucostigma nucleopolyhedrovirus, Ostreococcus virus OsV5, Paramecium bursaria Chlorella virus 1, Planctopirus limnophila DSM 3776, Plutella xylostella granulovirus, Prochlorococcus marinus, Pseudarthrobacter chlorophenolicus A6, Pseudomonas phage F8, Ralstonia phage RSB1, Saccharomyces cerevisiae, Sphingobacterium spiritivorum ATCC 33300, Spodoptera litura granulovirus, Staphylococcus epidermidis RP62A, Staphylothermus marinus F1, Stigmatella aurantiaca DW4/3-1, swinepox virus, Tetrahymena thermophila, Thermobaculum terrenum ATCC BAA-798, Thermofilum pendens Hrk 5, Vaccinia virus, Vibrio phage, Xanthomonas phage, Xylanimonas cellulosilytica DSM 15894
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