Overview for MACiE Entry M0202
EC Number: 184.108.40.206 (A member of the Ligases, Forming phosphoric-ester bonds, Ligases that form phosphoric-ester bonds (only sub-subclass identified to date))
Enzyme Name: DNA ligase (ATP)
Biological Species: Bacteriophage t7 (Virus)
Catalytic Chain UniprotKB Accession Codes:
Representative PDB Code: 1a0i - ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7 COMPLEX WITHATP (Resolution = 2.60 Å).
Display structure information
Overall Comment: Asp192 and Glu194 in Chlorella Virus DNA ligase homologous to Glu242 and Glu244 in this enzyme have been implicated in the ligase adenylation step. However their function has yet to fully understood . The Mg(II) cofactor is not present in the crystal structure.
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Stepwise Description of the Reaction
|Step 1||Lys34 acts as a nucleophile and attacks the alpha-phosphate of ATP in a substitution reaction, liberating pyrophosphate and forming an intermediate covalently bound to the enzyme. Mg(II), Lys238 and Lys240 stabilise the intermediates formed, Lys238 positions the pyrophosphate leaving group, allowing for the in-line mechanism to occur.|
|Step 2||The phosphate group of the first strand of DNA acts as a nucleophile and attacks the phosphate bound to Lys34 in a substitution reaction, liberating Lys34 and forming a DNA-AMP complex. Mg(II), Lys238 and Lys240 stabilise the intermediates formed.|
|Step 3||The AMP phosphate deprotonates the hydroxyl group of the second DNA molecule, which then acts as a nucleophile and attacks the DNA phosphate of the DNA-AMP complex in a substitution reaction, liberating AMP and the ligated DNA. Mg(II), Lys238 and Lys240 stabilise the intermediates formed.|
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Catalytic Residues Involved
||Location of Function
Metal Cofactors for M0202
||MG(not in PDB)
- I. R. Lehman (1974), Science, 186, 790-797. DNA ligase: structure, mechanism, and function.
- H. S. Subramanya et al. (1996), Cell, 85, 607-615. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
- A. J. Doherty et al. (2000), J. Mol. Biol., 296, 43-56. Nick recognition by DNA ligases.
- M. Odell et al. (2000), Mol. Cell, 6, 1183-1193. Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
- V. Sriskanda et al. (2002), J. Biol. Chem., 277, 9661-9667. Role of nucleotidyl transferase motif V in strand joining by chlorella virus DNA ligase.
Homologue information for M0202 (1a0i)
MACiE Homologues (within the PDB)
MACiE Homologues (within UniprotKB/SwissProt)
Links to this entry in other databases