Any feedback?
Please rate this page
(enzyme.php)
(0/150)

BRENDA support

BRENDA Home
show all | hide all No of entries

Information on EC 6.5.1.6 - DNA ligase (ATP or NAD+) and Organism(s) Thermococcus fumicolans and UniProt Accession Q9HH07

for references in articles please use BRENDA:EC6.5.1.6
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
IUBMB Comments
The enzymes from the archaea Thermococcus fumicolans and Thermococcus onnurineus show high activity with either ATP or NAD+, and significantly lower activity with TTP, GTP, and CTP. 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 or NAD+, 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. Different from EC 6.5.1.1, DNA ligase (ATP), EC 6.5.1.2, DNA ligase (NAD+) and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
Specify your search results
Select one or more organisms in this record: ?
This record set is specific for:
Thermococcus fumicolans
UNIPROT: Q9HH07
Show additional data
Do not include text mining results
Include (text mining) results
Include results (AMENDA + additional results, but less precise)
The taxonomic range for the selected organisms is: Thermococcus fumicolans
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
Synonyms
tfu dna ligase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate
show the reaction diagram
(1)
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide
show the reaction diagram
(2)
SYSTEMATIC NAME
IUBMB Comments
poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP or NAD+)
The enzymes from the archaea Thermococcus fumicolans and Thermococcus onnurineus show high activity with either ATP or NAD+, and significantly lower activity with TTP, GTP, and CTP. 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 or NAD+, 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. Different from EC 6.5.1.1, DNA ligase (ATP), EC 6.5.1.2, DNA ligase (NAD+) and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
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
the enzyme displays nick joining and blunt-end ligation activity using either ATP or NAD+, as a cofactor
-
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)n+m
show the reaction diagram
the enzyme displays nick joining and blunt-end ligation activity using either ATP or NAD+, as a cofactor
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
the enzyme does not require monovalent cations to be active. 2 mM KCl or up to 5 mM of NaCl increase its activity up to 70%. Higher concentrations of these cations are inhibitory, but the enzyme still retains 50% activity with 100 mM NaCl or 100 mM KCl
Mg2+
strongly dependent on the MgCl2. While optimal activity is obtained with 2 mM, it is almost totally inhibited with 10 mM MgCl2
Na+
the enzyme does not require monovalent cations to be active. 2 mM KCl or up to 5 mM of NaCl increase its activity up to 70%. Higher concentrations of these cations are inhibitory, but the enzyme still retains 50% activity with 100 mM NaCl or 100 mM KCl
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Mg2+
while optimal activity is obtained with 2 mM, it is almost totally inhibited with 10 mM MgCl2
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.16
ATP
pH 6.5, 55°C
0.69
NAD+
pH 6.5, 55°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5
about 80% of maximal activity, pH 7.0: optimum, pH 7.5: about 10% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 80
40°C: 50% of maximal activity, 80°C: about 50% of maximal activity
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DNLI_THEFM
559
0
63598
Swiss-Prot
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90
15 min, 50% loss of activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) pLysS
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Rolland, J.L.; Gueguen, Y.; Persillon, C.; Masson, J.M.; Dietrich, J.
Characterization of a thermophilic DNA ligase from the archaeon Thermococcus fumicolans
FEMS Microbiol. Lett.
236
267-273
2004
Thermococcus fumicolans (Q9HH07), Thermococcus fumicolans
Manually annotated by BRENDA team