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Overview for MACiE Entry M0202

Version history

General Information

EC Number: 6.5.1.1 (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).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of ATP

Image of DNA-5-phosphate

Image of DNA-3-hydroxyl

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Image of DNA

Image of diphosphate

Image of AMP

ATP
C00002
CHEBI:30616
DNA-5-phosphate
X00015
DNA-3-hydroxyl
X00016
DNA
C00039
CHEBI:4705
diphosphate
C00013
CHEBI:18361
AMP
C00020
CHEBI:456215

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 [5]. The Mg(II) cofactor is not present in the crystal structure.


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Stepwise Description of the Reaction

Step 1Lys34 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 2The 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 3The 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

Type Number Chain Location of Function
Lys 34 A Side Chain
Lys 238 A Side Chain
Lys 240 A Side Chain

Metal Cofactors for M0202

Type Het group Number Chain
magnesium MG(not in PDB) 1 x Overview

References

  1. I. R. Lehman (1974), Science, 186, 790-797. DNA ligase: structure, mechanism, and function.
    Medline: 4377758
  2. H. S. Subramanya et al. (1996), Cell, 85, 607-615. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
    Medline: 8653795
  3. A. J. Doherty et al. (2000), J. Mol. Biol., 296, 43-56. Nick recognition by DNA ligases.
    Medline: 10656817
  4. 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.
    Medline: 11106756
  5. 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.
    Medline: 11751916

Homologue information for M0202 (1a0i)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

GOA logo
nucleotide binding (molecular function)
DNA ligase activity (molecular function)
DNA ligase (ATP) activity (molecular function)
ATP binding (molecular function)
DNA replication (biological process)
DNA repair (biological process)
DNA recombination (biological process)
cellular response to DNA damage stimulus (biological process)
ligase activity (molecular function)
metal ion binding (molecular function)
DNA ligation involved in DNA repair (biological process)
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