CATH Classification

Domain Context

CATH Clusters

Superfamily Helix hairpin bin
Functional Family

Enzyme Information

6.5.1.2
DNA ligase (NAD(+)).
based on mapping to UniProt Q837V6
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)

Q837V6
DNLJ_ENTFA
Enterococcus faecalis V583
DNA ligase

PDB Structure

PDB 4LH6
External Links
Method X-RAY DIFFRACTION
Organism
Primary Citation
Identification through structure-based methods of a bacterial NAD(+)-dependent DNA ligase inhibitor that avoids known resistance mutations.
Murphy-Benenato, K., Wang, H., McGuire, H.M., Davis, H.E., Gao, N., Prince, D.B., Jahic, H., Stokes, S.S., Boriack-Sjodin, P.A.
Bioorg.Med.Chem.Lett.