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Information on EC 6.5.1.2 - DNA ligase (NAD+) and Organism(s) Geobacillus stearothermophilus and UniProt Accession O87703

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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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Geobacillus stearothermophilus
UNIPROT: O87703
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Word Map
The taxonomic range for the selected organisms is: Geobacillus stearothermophilus
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
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
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Deoxyribonucleate ligase
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-
-
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Deoxyribonucleic acid joinase
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-
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Deoxyribonucleic acid ligase
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-
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Deoxyribonucleic joinase
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-
-
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Deoxyribonucleic ligase
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-
-
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Deoxyribonucleic repair enzyme
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-
-
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Deoxyribonucleic-joining enzyme
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-
-
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DNA joinase
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-
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DNA ligase
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-
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DNA ligase (NAD)
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-
-
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DNA repair enzyme
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-
-
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DNA-joining enzyme
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-
-
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Ligase, polynucleotide (nicotinamide adenine dinucleotide)
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-
-
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Polydeoxyribonucleotide synthase (NAD+)
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-
-
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Polydeoxyribonucleotide synthase [NAD+]
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-
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Polynucleotide ligase
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-
-
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Polynucleotide synthetase
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-
-
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Polynucleotide synthetase (nicotinamide adenine dinucleotide)
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-
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Synthetase, polydeoxyribonucleotide (nicotinamide adenine dinucleotide)
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-
-
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Tfi DNA ligase
-
-
-
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Tth DNA ligase
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-
-
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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
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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
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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
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
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn2+
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bound to the C-terminal fragment
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_GEOSE
670
0
74231
Swiss-Prot
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30000
-
SDS-PAGE, C-terminal fragment
30040
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ESI-mass spectrometry, C-terminal fragment
35790
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ESI-mass spectrometry, N-terminal fragment
36000
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SDS-PAGE, N-terminal fragment
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour phase diffusion method, K114A mutant protein fragment
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
DELTA1-396
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no self adenylation activity, DNA-binding not affected
DELTA319-670
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full self adenylation activity but strongly reduced DNA-binding and ligation activity
K114A
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prevention of partial adenylation of the enzyme
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, 10% glycerol
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
fragments overexpressed in Escherichia coli
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
1-318 fragment with K114A mutation
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N-terminal fragment 1-318 and C-terminal fragment starting from position 397 seperately expressed in Escherichia coli BL21
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
NAD+-dependent ligases can serve as a valuable target in the development of chemotherapeutics for the treatment of numerous human ailments
medicine
-
potential target for antibiotics due to the fact that eukaryotic cells use ATP instead of NAD+ as cofactor for DNA-ligase
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Timson, D.J.; Wigley, D.B.
Functional domains of an NAD+-dependent DNA ligase
J. Mol. Biol.
285
73-83
1999
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Singleton, M.R.; Hakansson, K.; Timson, D.J.; Wigley, D.B.
Structure of the adenylation domain of an NAD+-dependent DNA ligase
Structure
7
35-42
1999
Geobacillus stearothermophilus
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