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Catalytic Site Atlas

CSA LITERATURE entry for 1dgs

E.C. nameDNA ligase (NAD+)
SpeciesThermus filiformis ()
E.C. Number (IntEnz) 6.5.1.2
CSA Homologues of 1dgsThere are 13 Homologs
CSA Entries With UniProtID Q9ZHI0
CSA Entries With EC Number 6.5.1.2
PDBe Entry 1dgs
PDBSum Entry 1dgs
MACiE Entry 1dgs

Literature Report

IntroductionDNA ligases catalyse the formation of phosphodiester bonds at single-strand breaks in double stranded DNA and are required in DNA replication, repair and recombination. DNA ligases are also used extensively for in vitro DNA manipulation and cloning techniques. Eukaryotic, viral and achaebacteria encoded enzyme al require ATP, where as NAD+ requiring DNA ligases are found exclusively in eubacteria.
MechansimThe overall mechanism involves three reversible steps. The nicked DNA substrate is formed by annealing two short oligonucleotides to a longer complementary oligonucleotide. First, a covalently adenylated enzyme intermediate is formed by the transfer of the adenylate group of NAD+ to the E-amino group of Lys116. Second, the adenylate moiety is transferred from the enzyme to the 5'-terminal phosphate on one of the oligomers (oligomer A). Finally, a phosphodiester bond is formed by a nucleophilic attack of the 3'-hydroxyl terminus of the other oligomer (oligomer B) on the activated 5'-phosphoryl group of oligomer A in an Sn2 like mechanism with a pentavalent phosphorous transition state.
Two Mg(2+) binding sites have been identified within the catalytic site (although the metals are not present in the pdb 1dgs) . The positive charge stabilises the developing negative charge of the pentavalent transition state and also the charged reaction intermediates.
Reaction

Catalytic Sites for 1dgs

Literature References

Notes:
Luo J
Identification of essential residues in Thermus thermophilus DNA ligase.
Nucleic Acids Res 1996 24 3079-3085
PubMed: 8760897
Doherty AJ
Structural and mechanistic conservation in DNA ligases.
Nucleic Acids Res 2000 28 4051-4058
PubMed: 11058099
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