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Literature summary for 6.5.1.2 extracted from

  • Lee, J.Y.; Chang, C.; Song, H.K.; Moon, J.; Yang, J.K.; Kim, H.K.; Kwon, S.T.; Suh, S.W.
    Crystal structure of NAD+-dependent DNA ligase: modular architecture and functional implications (2000), EMBO J., 19, 1119-1129.
    View publication on PubMedView publication on EuropePMC

Application

Application Comment Organism
medicine potential target for antibiotics Thermus filiformis

Cloned(Commentary)

Cloned (Comment) Organism
native and selenomethionine-substituted enzyme Thermus filiformis

Crystallization (Commentary)

Crystallization (Comment) Organism
vapor diffusion method Thermus filiformis

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Thermus filiformis
Zn2+ 1 mol per mol of enzyme, Cys406, Cys409, Cys422 and Cys427 form a zinc binding motif Thermus filiformis

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
75940
-
calculated from DNA-sequence Thermus filiformis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Thermus filiformis DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?

Organism

Organism UniProt Comment Textmining
Thermus filiformis Q9ZHI0
-
-

Purification (Commentary)

Purification (Comment) Organism
-
Thermus filiformis

Reaction

Reaction Comment Organism Reaction ID
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide 3 steps of reaction: 1. adenylation of the ligase in the presence of NAD+, 2. transferring the adenylate moiety to the 5'-phosphate of the nicked DNA substrate, 3. sealing the nick through the formation of a phosphodiester bond Thermus filiformis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
Thermus filiformis AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m DNA-repair, phosphodiester bond formation between adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA Thermus filiformis AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
?

Subunits

Subunits Comment Organism
monomer
-
Thermus filiformis

Cofactor

Cofactor Comment Organism Structure
NAD+ required Thermus filiformis