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Information on EC 6.5.1.1 - DNA ligase (ATP)

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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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UNIPROT: O41026
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Word Map
The enzyme appears in viruses and cellular organisms
Reaction Schemes
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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
ChVLig
Paramecium bursaria chlorella virus
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DNA ligase
Paramecium bursaria chlorella virus
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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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Deoxyribonucleic joinase
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Deoxyribonucleic ligase
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Deoxyribonucleic repair enzyme
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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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Polynucleotide ligase
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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 hide
9015-85-4
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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)n+m
show the reaction diagram
Paramecium bursaria chlorella virus
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
Paramecium bursaria chlorella virus
10 mM, standard reaction condition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 1
ATP
Paramecium bursaria chlorella virus
pH 7.5, 22°C, wild-type, Vmax: 1.1/sec
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
Paramecium bursaria chlorella virus
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
Paramecium bursaria chlorella virus
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Paramecium bursaria chlorella virus
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UniProt
Manually annotated by BRENDA team
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CDELTA1
Paramecium bursaria chlorella virus
mutant with deleted C-terminal five amino acids: mutant shows 34% the specific activity of wild-type. Preformed Lig-AMP in vivo: 71% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 8% of total enzyme (wild-type: 21%)
CDELTA2
Paramecium bursaria chlorella virus
mutant with deleted C-terminal five amino acids: mutant shows 6% the specific activity of wild-type. Preformed Lig-AMP in vivo: 80% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 1.1% of total enzyme (wild-type: 21%)
CDELTA3
Paramecium bursaria chlorella virus
mutant with deleted C-terminal five amino acids: mutant shows 2% the specific activity of wild-type. Preformed Lig-AMP in vivo: 67% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 1.3% of total enzyme (wild-type: 21%)
CDELTA4
Paramecium bursaria chlorella virus
mutant with deleted C-terminal five amino acids: mutant shows 1% the specific activity of wild-type. Preformed Lig-AMP in vivo: 18% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 0.8% of total enzyme (wild-type: 21%)
CDELTA5
Paramecium bursaria chlorella virus
mutant with deleted C-terminal five amino acids: mutant shows 1% the specific activity of wild-type and is poorly responsive to ATP. Preformed Lig-AMP in vivo: 7% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 0.5% of total enzyme (wild-type: 21%)
D297A
Paramecium bursaria chlorella virus
preformed Lig-AMP in vivo: 76% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 2.9% of total enzyme (wild-type: 21%)
D297E
Paramecium bursaria chlorella virus
preformed Lig-AMP in vivo: 74% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 1.8% of total enzyme (wild-type: 21%)
D297N
Paramecium bursaria chlorella virus
preformed Lig-AMP in vivo: 60% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 2.8% of total enzyme (wild-type: 21%)
R293A
Paramecium bursaria chlorella virus
preformed Lig-AMP in vivo: 52% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 1.9% of total enzyme (wild-type: 21%)
R293K
Paramecium bursaria chlorella virus
preformed Lig-AMP in vivo: 70% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 3.4% of total enzyme (wild-type: 21%)
R293Q
Paramecium bursaria chlorella virus
preformed Lig-AMP in vivo: 48% of total enzyme (wild-type: 70%), preformed Lig-AMP in vitro: 3.8% of total enzyme (wild-type: 21%)
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
using Ni-NTA chromatography
Paramecium bursaria chlorella virus
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli as a His-tagged fusion protein
Paramecium bursaria chlorella virus
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Samai, P.; Shuman, S.
Kinetic analysis of DNA strand joining by Chlorella virus DNA ligase and the role of nucleotidyltransferase motif VI in ligase adenylylation
J. Biol. Chem.
287
28609-28618
2012
Paramecium bursaria chlorella virus (O41026)
Manually annotated by BRENDA team