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IUBMB CommentsThe enzymes from the archaea Hyperthermus butylicus and Sulfophobococcus zilligii are active with ATP, ADP or GTP. They show no activity with NAD+. 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, ADP, or GTP, forming a phosphoramide bond between adenylate/guanylate and a lysine residue. The nucleotide is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine/guanosine)-[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 nucleotide. Different from EC 6.5.1.1, DNA ligase (ATP), and EC 6.5.1.6, DNA ligase (ATP or NAD+), which cannot utilize GTP.
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(deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
(deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP
(3c)
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5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
5'-guanosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(3b)
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ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate
ADP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + phosphate
(2a)
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ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate
ATP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + diphosphate
(1a)
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GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP + diphosphate
GTP + [DNA ligase]-L-lysine = 5'-guanosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + diphosphate
(3a)
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(deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
(1c)
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(deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
catalytic reaction mechanism, detailed overview
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5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(1b)
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5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(2b)
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ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate
(2)
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ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate
(2)
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ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate
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ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate
(1)
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ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate
(1)
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ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate
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GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP + diphosphate
(3)
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GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP + diphosphate
(3)
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GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP + diphosphate
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ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
additional information
?
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ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
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the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
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?
ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
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95% nick-closing activity when compared with ATP
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?
ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
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multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
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?
ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
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72% nick-closing activity as compared with ATP
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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nick-closing activity
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
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nick-closing activity
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
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?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
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the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
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?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
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86% nick-closing activity when compared with ATP
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?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
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the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
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-
?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
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86% nick-closing activity when compared with ATP
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?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
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?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
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63% nick-closing activity as compared with ATP
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?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
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?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
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63% nick-closing activity as compared with ATP
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?
additional information
?
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no activity with NAD+, CTP or TTP
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?
additional information
?
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no activity with NAD+, CTP or TTP
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?
additional information
?
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activity with CTP, TTP or NAD+ is lees than 5% compared to the activity with ATP
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?
additional information
?
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activity with CTP, TTP or NAD+ is lees than 5% compared to the activity with ATP
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?
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ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
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the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
-
-
?
ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + phosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
-
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
-
-
?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
-
the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
-
-
?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
-
the multiple cofactor specificity of the the enzyme may possibly be attributed to the ease of ATP decomposition at the high temperatures at which hyperthermophiles grow
-
-
?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
-
-
?
GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
GMP + diphosphate + (deoxyribonucleotide)n+m
-
multiple cofactor specificity of the DNA ligase from Sulfophobococcus zilligii may possibly be attributed to the ease of decomposition of ATP at the high temperatures. Due to limited amount of ATP, other NTPs might have been employed as alternative energy sources. This unique biochemical feature seems to have evolved to permit survival under unusual conditions
-
-
?
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Sun, Y.; Seo, M.S.; Kim, J.H.; Kim, Y.J.; Kim, G.A.; Lee, J.I.; Lee, J.H.; Kwon, S.T.
Novel DNA ligase with broad nucleotide cofactor specificity from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii: influence of ancestral DNA ligase on cofactor utilization
Environ. Microbiol.
10
3212-3224
2008
Sulfophobococcus zilligii, Sulfophobococcus zilligii DSM Z 11193
brenda
Supangat, S.; An, Y.J.; Sun, Y.; Kwon, S.T.; Cha, S.S.
Purification, crystallization and preliminary crystallographic analysis of a multiple cofactor-dependent DNA ligase from Sulfophobococcus zilligii
Acta Crystallogr. Sect. F
66
1583-1585
2010
Sulfophobococcus zilligii
brenda
Kim, J.H.; Lee, K.K.; Sun, Y.; Seo, G.J.; Cho, S.S.; Kwon, S.H.; Kwon, S.T.
Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance
Extremophiles
17
515-522
2013
Hyperthermus butylicus, Hyperthermus butylicus DSM Z 5456
brenda