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Information on EC 6.5.1.2 - DNA ligase (NAD+) and Organism(s) Thermus filiformis and UniProt Accession Q9ZHI0

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EC Tree
IUBMB Comments
The enzyme, typically found in bacteria, 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 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. RNA can also act as substrate, to some extent. cf. EC 6.5.1.1, DNA ligase (ATP), 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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Thermus filiformis
UNIPROT: Q9ZHI0
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The taxonomic range for the selected organisms is: Thermus filiformis
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
+
beta-nicotinamide D-nucleotide
+
+
5'-phospho-(deoxyribonucleotide)m
=
+
+
beta-nicotinamide D-nucleotide
Synonyms
nad(+)-dependent dna ligase, taq dna ligase, nad+-dependent dna ligase, tfi dna ligase, nad-dependent dna ligase, tth dna ligase, mimilig, mtuliga, wbm-liga, polynucleotide synthetase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
NAD+-dependent DNA ligase
-
Deoxyribonucleate ligase
-
-
-
-
Deoxyribonucleic acid joinase
-
-
-
-
Deoxyribonucleic acid ligase
-
-
-
-
Deoxyribonucleic joinase
-
-
-
-
Deoxyribonucleic ligase
-
-
-
-
Deoxyribonucleic repair enzyme
-
-
-
-
Deoxyribonucleic-joining enzyme
-
-
-
-
DNA joinase
-
-
-
-
DNA ligase
DNA ligase (NAD)
-
-
-
-
DNA repair enzyme
-
-
-
-
DNA-joining enzyme
-
-
-
-
Ligase, polynucleotide (nicotinamide adenine dinucleotide)
-
-
-
-
NAD+-dependent DNA ligase
-
-
Polydeoxyribonucleotide synthase (NAD+)
-
-
-
-
Polydeoxyribonucleotide synthase [NAD+]
-
-
-
-
Polynucleotide ligase
-
-
-
-
Polynucleotide synthetase
-
-
-
-
Polynucleotide synthetase (nicotinamide adenine dinucleotide)
-
-
-
-
Synthetase, polydeoxyribonucleotide (nicotinamide adenine dinucleotide)
-
-
-
-
Tfi DNA ligase
-
-
-
-
Tth DNA ligase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide
show the reaction diagram
3 steps of reaction: 1. adenylation of the ligase in the presence of NAD+, 2. transferring the adenylate moiety to the 5'-phosphate of the nicked DNA substrate, 3. sealing the nick through the formation of a phosphodiester bond
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide
show the reaction diagram
3 steps of reaction: 1. adenylation of the ligase in the presence of NAD+, 2. transferring the adenylate moiety to the 5'-phosphate of the nicked DNA substrate, 3. sealing the nick through the formation of a phosphodiester bond
-
SYSTEMATIC NAME
IUBMB Comments
poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (NAD+)
The enzyme, typically found in bacteria, 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 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. RNA can also act as substrate, to some extent. cf. EC 6.5.1.1, DNA ligase (ATP), 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
37259-52-2
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
show the reaction diagram
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
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
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
show the reaction diagram
DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
show the reaction diagram
-
DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn2+
1 mol per mol of enzyme, Cys406, Cys409, Cys422 and Cys427 form a zinc binding motif
Ca2+
-
activates wild-type enzyme and mutant enzyme DELTA582-667
Mg2+
-
best metal-activator of wild-type enzyme and mutant enzyme DELTA582-667
Mn2+
-
activates wild-type enzyme and mutant enzyme DELTA582-667
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
-
wild-type enzyme
8.5
-
mutant enzyme DELTA582-667
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70
-
mutant enzyme DELTA582-667 and wild-type enzyme, activity of mutant enzyme DELTA582-667 is 50% of wild-type activity
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50 - 80
-
50°C: about 50% of maximal activity of wild-type enzyme and of mutant enzyme DELTA582-667, 80°C: about 50% of maximal activity of wild-type enzyme and mutant enzyme DELTA582-667
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?
DNLJ_THEFI
670
0
76594
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
75940
calculated from DNA-sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
vapor diffusion method
microseeding technique
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
DELTA582-667
-
lower thermal stability than wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70
-
wild-type enzyme is stable for 40 min, about 20% loss of activity after 180 min. Mutant enzyme DELTA582-667 loses 20% of its activity after 80 min and 90% of its activity after 170 min
90
-
wild-type enzyme is stable for 20 min, about 50% loss of activity after 100 min. Mutant enzyme DELTA582-667 loses 30% of its initial activity after 40 min, completely loses activity after 80 min
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant protein
-
wild-type and mutants expressed in Escherichia coli
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
native and selenomethionine-substituted enzyme
deletion mutants, expression in Escherichia coli
-
expressed in Escherichia coli BL26
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lee, J.Y.; Kim, H.K.; Chang, C.; Eom, S.H.; Hwang, K.Y.; Cho, Y.; Yu, Y.G.; Ryu, S.E.; Kwon, S.T.; Suh, S.W.
Crystallization and preliminary x-ray crystallographic analysis of NAD+-dependent DNA ligase from Thermus filiformis
Acta Crystallogr. Sect. D
D56
357-358
2000
Thermus filiformis
-
Manually annotated by BRENDA team
Lee, J.Y.; Chang, C.; Song, H.K.; Moon, J.; Yang, J.K.; Kim, H.K.; Kwon, S.T.; Suh, S.W.
Crystal structure of NAD+-dependent DNA ligase: modular architecture and functional implications
EMBO J.
19
1119-1129
2000
Thermus filiformis (Q9ZHI0), Thermus filiformis
Manually annotated by BRENDA team
Jeon, H.J.; Shin, H.J.; Choi, J.J.; Hoe, H.S.; Kim, H.K.; Suh, S.W.; Kwon, S.T.
Mutational analyses of the thermostable NAD+-dependent DNA ligase from Thermus filiformis
FEMS Microbiol. Lett.
237
111-118
2004
Thermus filiformis
Manually annotated by BRENDA team
Tomkinson, A.E.; Vijayakumar, S.; Pascal, J.M.; Ellenberger, T.
DNA ligases: Structure, reaction mechanism, and function
Chem. Rev.
106
687-699
2006
Enterococcus faecalis (Q837V6), Thermus filiformis (Q9ZHI0)
Manually annotated by BRENDA team
Pascal, J.M.
DNA and RNA ligases: structural variations and shared mechanisms
Curr. Opin. Struct. Biol.
18
96-105
2008
Escherichia coli, Enterococcus faecalis, Thermus filiformis
Manually annotated by BRENDA team
Dwivedi, N.; Dube, D.; Pandey, J.; Singh, B.; Kukshal, V.; Ramachandran, R.; Tripathi, R.P.
NAD+-dependent DNA ligase: a novel target waiting for the right inhibitor
Med. Res. Rev.
28
545-568
2008
Escherichia coli, Geobacillus stearothermophilus (O87703), Mycobacterium tuberculosis (P9WNV1), Enterococcus faecalis (Q837V6), Thermus filiformis (Q9ZHI0), Mycobacterium tuberculosis H37Rv (P9WNV1)
Manually annotated by BRENDA team