Ligases;
Forming phosphoric-ester bonds;
Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)
BRITE hierarchy

poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP, ADP or GTP)

(1) ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate (overall reaction) [RN:R00381];
(1a) ATP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + diphosphate;
(1b) 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine;
(1c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP;
(2) ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate (overall reaction) [RN:R10822];
(2a) ADP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + phosphate;
(2b) 5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine;
(2c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP;
(3) GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP + diphosphate (overall reaction) [RN:R10823];
(3a) GTP + [DNA ligase]-L-lysine = 5'-guanosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + diphosphate;
(3b) 5'-guanosyl [DNA ligase]-Nepsilon-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine;
(3c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP

R00381 R10822 R10823
Reaction

ATP [CPD:C00002];
(deoxyribonucleotide)n-3'-hydroxyl;
5'-phospho-(deoxyribonucleotide)m;
[DNA ligase]-L-lysine;
5'-adenosyl [DNA ligase]-Nepsilon-phosphono-L-lysine;
5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m;
ADP [CPD:C00008];
GTP [CPD:C00044];
5'-guanosyl [DNA ligase]-Nepsilon-phosphono-L-lysine;
5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m

The 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.

EC 6.5.1.7 created 2014, modified 2016