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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Aeropyrum pernix and UniProt Accession Q9YD18

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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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Aeropyrum pernix
UNIPROT: Q9YD18
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The taxonomic range for the selected organisms is: Aeropyrum pernix
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
ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
show the reaction diagram
activity with ADP is slightly lower than with ATP
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
show the reaction diagram
the enzyme is inactive when ATP was substituted by AMP or NAD+
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
the enzyme requires Mg2+ or Mn2+ for activity, Ca2+ or Co2+ are less effective
Co2+
the enzyme requires Mg2+ or Mn2+ for activity, Ca2+ or Co2+ are less effective
KCl
optimum concentration: 5 mM
Mg2+
optimal concentration: 15 mM, the enzyme requires Mg2+ or Mn2+ for activity, Ca2+ or Co2+ are less effective
Mn2+
optimal concentration: 7.5 mM, the enzyme requires Mg2+ or Mn2+ for activity, Ca2+ or Co2+ are less effective
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
KCl
100 mM, approximately 70% inhibition
NaCl
100 mM, approximately 70% inhibition
NH4Cl
100 mM, approximately 70% inhibition
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
optimum for nick-closing activity
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8.2
80% of maximal activity is observed between pH 7.0 and 8.2
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70
optimum for nick-closing activity is above 70°C
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
65 - 80
in the nick-closing assay, the recombinant ligase shows more than 80% activity in the temperature range 65-80°C. Ligase activity declines at temperatures below 35°C. A drastic decrease in activity is observed between 80 and 90°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
the ApeLig gene is originally annotated as a protein of 619 amino acids, with a calculated mass of 69196.2 Da. Later it was reannotated as a protein of 602 amino acids (67747.6 Da), in which 17 amino acids are truncated from the N-terminus of the originally annotated protein. The UniProt-number refers to the 602 amino acid protein
SwissProt
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
69000
1 * 69000, SDS-PAGE
69196
1 * 69196, the authors refer to the protein of 619 amino acids that is later reannotated as a protein of 602 amino acids (67747.6 Da), calculated from sequence
70000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
F115A
the ApeLig gene is originally annotated as a protein of 619 amino acids, with a calculated mass of 69196.2 Da. Later it was reannotated as a protein of 602 amino acids (67747.6 Da), in which 17 amino acids are truncated from the N-terminus of the originally annotated protein. The authors of this reference refer to the 619 amino acid protein containing the mutation at position F132. According to the UniProt numbering the position of this mutation is 115. Surface plasmon resonance analyses reveals that the F132A mutant does not interact with an immobilized subunit of the proliferating cell nuclear antigen (which is known as a DNA sliding clamp that acts as a platform for the assembly of enzymes involved in DNA replication and repair). No stimulation of the ligation activity of the F132A protein by the proliferating cell nuclear antigen can be detected in vitro. These results indicate that the phenylalanine, which is located the predicted proliferating cell nuclear antigen-binding region in the ligase, has a critical role for the physical and functional interaction with proliferating cell nuclear antigen
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
100
stable for 60 min, half-life: 25 min
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
Kiyonari, S.; Kamigochi, T.; Ishino, Y.
A single amino acid substitution in the DNA-binding domain of Aeropyrum pernix DNA ligase impairs its interaction with proliferating cell nuclear antigen
Extremophiles
11
675-684
2007
Aeropyrum pernix (Q9YD18), Aeropyrum pernix, Aeropyrum pernix DSM 11879 (Q9YD18)
Manually annotated by BRENDA team
Jeon, S.J.; Ishikawa, K.
A novel ADP-dependent DNA ligase from Aeropyrum pernix K1
FEBS Lett.
550
69-73
2003
Aeropyrum pernix (Q9YD18), Aeropyrum pernix, Aeropyrum pernix DSM 11879 (Q9YD18)
Manually annotated by BRENDA team