CATH Classification
| Level | CATH Code | Description |
|---|---|---|
|
2 | Mainly Beta |
|
2.40 | Beta Barrel |
|
2.40.50 | OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
|
2.40.50.140 | Nucleic acid-binding proteins |
Domain Context
CATH Clusters
| Superfamily | Nucleic acid-binding proteins |
| Functional Family | Probable ATP-dependent DNA ligase |
Enzyme Information
| 6.5.1.1 |
DNA ligase (ATP).
based on mapping to UniProt P9WNV3
ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.
-!- The enzyme 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 ATP, 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 6.5.1.2, EC 6.5.1.6 and EC 6.5.1.7.
|
UniProtKB Entries (1)
| P9WNV3 |
LIGD_MYCTU
Mycobacterium tuberculosis H37Rv
Multifunctional non-homologous end joining DNA repair protein LigD
|
PDB Structure
| PDB | 1VS0 |
| External Links | |
| Method | X-RAY DIFFRACTION |
| Organism | Escherichia |
| Primary Citation |
Crystal Structure and Nonhomologous End-joining Function of the Ligase Component of Mycobacterium DNA Ligase D.
J.Biol.Chem.
|
