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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Methanothermobacter thermautotrophicus and UniProt Accession Q50566

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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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Methanothermobacter thermautotrophicus
UNIPROT: Q50566
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The taxonomic range for the selected organisms is: Methanothermobacter thermautotrophicus
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)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
dATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
dAMP + diphosphate + (deoxyribonucleotide)m+n
show the reaction diagram
strandjoining on a singly nicked DNA in the presence of a divalent cation and dATP, approx. 10% of activity with ATP
-
?
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
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
10 mM, divalent cation required for activity
Mg2+
10 mM, divalent cation required for activity
Mn2+
10 mM, divalent cation required for activity
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ammonium sulfate
10 mM, 60% inhibition
NaCl
50 mM, 75% inhibition, 80 mM, 90% inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9
approx. 20% of maximal activity at pH 6.5, approx. 90% of maximal activity at pH 9.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22 - 80
almost no activity at 22°C, approx. 25% of maximal activity at 40°C and 70°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
68000
zonal velocity sedimentation
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D253A
mutant DNA ligase reacts with ATP to form the covalent intermediate, but is unable to catalyze the full ligation reaction
K251A
no DNA ligase-adenylate formation and no nick-joining
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sriskanda, V.; Kelman, Z.; Hurwitz, J.; Shuman, S.
Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum
Nucleic Acids Res.
28
2221-2228
2000
Methanothermobacter thermautotrophicus (Q50566), Methanothermobacter thermautotrophicus
Manually annotated by BRENDA team