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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Thermococcus kodakarensis and UniProt Accession Q9HHC4

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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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Thermococcus kodakarensis
UNIPROT: Q9HHC4
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Word Map
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The taxonomic range for the selected organisms is: Thermococcus kodakarensis
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
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ATP
+
(deoxyribonucleotide)n-3'-hydroxyl
+
5'-phospho-(deoxyribonucleotide)m
=
(deoxyribonucleotide)n+m
+
AMP
+
diphosphate
+
+
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
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Deoxyribonucleate ligase
-
-
-
-
Deoxyribonucleic acid joinase
-
-
-
-
Deoxyribonucleic acid ligase
-
-
-
-
Deoxyribonucleic acid repair enzyme
-
-
-
-
Deoxyribonucleic acid-joining enzyme
-
-
-
-
Deoxyribonucleic joinase
-
-
-
-
Deoxyribonucleic ligase
-
-
-
-
Deoxyribonucleic repair enzyme
-
-
-
-
Deoxyribonucleic-joining enzyme
-
-
-
-
DNA joinase
-
-
-
-
DNA ligase
-
-
-
-
DNA ligase I
-
-
-
-
DNA ligase II
-
-
-
-
DNA ligase III
-
-
-
-
DNA ligase IV homolog
-
-
-
-
DNA repair enzyme
-
-
-
-
DNA-joining enzyme
-
-
-
-
Lig(Tk)
-
-
-
-
Pfu DNA ligase
-
-
-
-
Polydeoxyribonucleotide synthase (ATP)
-
-
-
-
Polydeoxyribonucleotide synthase [ATP]
-
-
-
-
Polynucleotide ligase
-
-
-
-
Sealase
-
-
-
-
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)30 + (deoxyribonucleotide)40
AMP + diphosphate + (deoxyribonucleotide)70
show the reaction diagram
ligTK displays little but significant ativity with NAD+
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
ATP + nicked DNA
AMP + diphosphate + ?
show the reaction diagram
-
-
-
-
?
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
AMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
monovalent cations stimulate activity, maximal activation at 10-30 mM
Mg2+
required for activity, maximal activity at 14-18 mM
Ca2+
-
9% of activity with Mg2+, maximal activity at 5 mM, inhibition above 40 mM
Mg2+
-
divalent cation required for activity, maximal activity at 15 mM
Mn2+
-
65% of activity with Mg2+, maximal activity at 25 mM
Sr2+
-
40% of activity with Mg2+, maximal activity at 25 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ca2+
-
inhibition above 40 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0014
nicked DNA
-
80°C, pH 8.0
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.11
nicked DNA
-
80°C, pH 8.0
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
65
at 0.00002 mM ligTK
70 - 80
at 0.0002 mM ligTK
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 100
at 0.0002 mM ligTK
35 - 80
at 0.00002 mM ligTK
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
52100
gel filtration
64079
1 * 64079, deduced from nucleotide sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
1 * 64079, deduced from nucleotide sequence
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant ligTK, ResourceQ, ResourceS, Superdex-200
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Nakatani, M.; Ezaki, S.; Atomi, H.; Imanaka, T.
Substrate recognition and fidelity of strand joining by an archaeal DNA ligase
Eur. J. Biochem.
269
650-656
2002
Thermococcus kodakarensis
Manually annotated by BRENDA team
Nakatani, M.; Ezaki, S.; Atomi, H.; Imanaka, T.
A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity
J. Bacteriol.
182
6424-6433
2000
Thermococcus kodakarensis (Q9HHC4)
Manually annotated by BRENDA team