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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Rattus norvegicus
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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: Rattus norvegicus
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
-
-
-
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Deoxyribonucleic acid joinase
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-
-
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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
-
-
-
-
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
-
-
-
-
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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-
-
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DNA repair enzyme
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-
-
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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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-
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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
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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
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
ATPalphaS + (deoxyribonucleotide)n + (deoxyribonucleotide)m
?
-
DNA ligase II can use ATPalphaS much more efficiently than DNA ligase I
-
-
?
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
-
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
DNA ligase II can use oligo(dT)*poly(rA) as substrate, DNA ligase I not
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
novel form of enzyme different from DNA ligase I: has a unique binding site, which has an absolute requirement for single-strand breaks, unable to join blunt-ended DNA, even in the presence of polyethylene glycol concentrations which stimulate such joining by DNA ligase I and T4 DNA ligase, the enzyme lacks the AMP-dependent nicking/closing reaction
-
?
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
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Anthracycline derivatives
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inhibit human DNA ligase I and rat DNA ligase I and III in the poly[d(A-T)] joining assay
Distamycin
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and derivatives, inhibit human DNA ligase I and rat DNA ligase I and III in the poly[d(A-T)] joining assay
additional information
-
antibodies raised against the 130000 MW polypeptide of DNA ligase I specifically recognize this species in an immunoblot and inhibit only the activity of DNA ligase I
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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
-
aging neurons are unable to affect base excision repair due to deficiency of DNA-ligase and DNA polymerase beta
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_RAT
918
0
102482
Swiss-Prot
other Location (Reliability: 3)
Q5U2M4_RAT
943
0
105443
TrEMBL
other Location (Reliability: 4)
A0A8I6A998_RAT
939
0
104295
TrEMBL
other Location (Reliability: 2)
F1M8E6_RAT
902
0
100344
TrEMBL
other Location (Reliability: 3)
Q566D8_RAT
913
0
101875
TrEMBL
other Location (Reliability: 3)
D4A0U6_RAT
911
0
104496
TrEMBL
other Location (Reliability: 5)
A0A096MKE9_RAT
961
0
107910
TrEMBL
other Location (Reliability: 4)
F7FP17_RAT
956
0
106821
TrEMBL
other Location (Reliability: 4)
A0A0G2JV76_RAT
1015
0
113395
TrEMBL
other Location (Reliability: 4)
A0A8J8XFV7_RAT
928
0
103634
TrEMBL
other Location (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
100000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, saturated ammonium sulfate solution buffered at pH 7.5, stable for several months
-
PURIFICATION (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
Mezzina, M.; Rossignol, J.M.; Philippe, M.; Izzo, R.; Bertazzoni, U.; Sarasin, A.
Mammalia DNA ligase. Structure and function in rat-liver tissues
Eur. J. Biochem.
162
325-332
1987
Rattus norvegicus
Levin, C.J.; Zimmerman, S.B.
A DNA ligase from mitochondria of rat liver
Biochem. Biophys. Res. Commun.
69
514-520
1976
Rattus norvegicus
Montecucco, A.; Lestingi, M.; Rossignol, J.M.; Elder, R.H.; Ciarrocchi, G.
Lack of discrimination between DNA ligase I and III by two classes of inhibitors, anthracyclines and distamycin
Biochem. Pharmacol.
45
1536-1539
1993
Homo sapiens, Rattus norvegicus
Husain, I.; Tomkinson, A.E.; Burkhart, W.A.; Moyer, M.B.; Ramos, W.; Mackey, Z.B.; Besterman, J.M.; Chen, J.
Purification and characterization of DNA ligase III from bovine testes. Homology with DNA ligase II and vaccinia DNA ligase
J. Biol. Chem.
270
9683-9690
1995
Tequatrovirus T4, Bos taurus, Rattus norvegicus
Elder, R.H.; Montecucco, A.; Carrocchi, G.; Rossignol, J.M.
Rat liver DNA ligase. Catalytic properties of a novel form of DNA ligase
Eur. J. Biochem.
203
53-58
1992
Rattus norvegicus
Elder, R.H.; Rossignol, J.M.
DNA ligases from rat liver. Purification and partial characterization of two molecular forms
Biochemistry
29
6009-6017
1990
Rattus norvegicus
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