CATH Classification
| Level | CATH Code | Description |
|---|---|---|
|
1 | Mainly Alpha |
|
1.10 | Orthogonal Bundle |
|
1.10.150 | DNA polymerase; domain 1 |
|
1.10.150.20 | 5' to 3' exonuclease, C-terminal subdomain |
Domain Context
CATH Clusters
| Superfamily | 5' to 3' exonuclease, C-terminal subdomain |
| Functional Family | DNA ligase |
Enzyme Information
| 6.5.1.2 |
DNA ligase (NAD(+)).
based on mapping to UniProt P15042
NAD(+) + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + beta- nicotinamide D-nucleotide.
-!- The enzyme, typically found in bacteria, catalyzes 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 catalyzes 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, EC 6.5.1.6 and EC 6.5.1.7.
|
UniProtKB Entries (1)
| P15042 |
DNLJ_ECOLI
Escherichia coli K-12
DNA ligase
|
PDB Structure
| PDB | 5TT5 |
| External Links | |
| Method | X-RAY DIFFRACTION |
| Organism | |
| Primary Citation |
Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases.
Proc. Natl. Acad. Sci. U.S.A.
|
