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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Saccharolobus solfataricus and UniProt Accession Q980T8

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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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Saccharolobus solfataricus
UNIPROT: Q980T8
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The taxonomic range for the selected organisms is: Saccharolobus solfataricus
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
ATP-dependent DNA ligase 1
-
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-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m
(deoxyribonucleotide)n+m + AMP + diphosphate
show the reaction diagram
-
-
-
?
ATP + [DNA ligase]-L-lysine
[DNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
show the reaction diagram
-
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
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-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m
(deoxyribonucleotide)n+m + AMP + diphosphate
show the reaction diagram
-
-
-
?
ATP + [DNA ligase]-L-lysine
[DNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
proliferating cell nuclear antigen
-
-
additional information
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor diffusion, crystal structures in conjunction with solution structures of these proteins based on small-angle X-ray scattering. In the absence of nicked DNA, the Sulfolobus solfataricus DNA ligase has an open, extended conformation. When complexed with heterotrimeric proliferating cell nuclear antigen, the DNA ligase binds to the proliferating cell nuclear antigen 3 subunit and ligase retain an open, extended conformation
in complex with the AMP-DNA reaction intermediate
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HisTrap column chromatography, and Superose 10/300 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli Rosetta (DE3) cells
expression in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Pascal, J.M.
DNA and RNA ligases: structural variations and shared mechanisms
Curr. Opin. Struct. Biol.
18
96-105
2008
Homo sapiens, Pyrococcus furiosus, Saccharolobus solfataricus
Manually annotated by BRENDA team
Pascal, J.M.; Tsodikov, O.V.; Hura, G.L.; Song, W.; Cotner, E.A.; Classen, S.; Tomkinson, A.E.; Tainer, J.A.; Ellenberger, T.
A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA
Mol. Cell.
24
279-291
2006
Saccharolobus solfataricus (Q980T8), Saccharolobus solfataricus, Saccharolobus solfataricus P2 (Q980T8)
Manually annotated by BRENDA team
Cannone, G.; Xu, Y.; Beattie, T.; Bell, S.; Spagnolo, L.
The architecture of an Okazaki fragment-processing holoenzyme from the archaeon Sulfolobus solfataricus
Biochem. J.
465
239-245
2015
Saccharolobus solfataricus (Q980T8), Saccharolobus solfataricus
Manually annotated by BRENDA team