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Literature summary for 6.5.1.2 extracted from

  • Lim, J.H.; Choi, J.; Kim, W.; Ahn, B.Y.; Han, Y.S.
    Mutational analyses of Aquifex pyrophilus DNA ligase define essential domains for self-adenylation and DNA binding activity (2001), Arch. Biochem. Biophys., 388, 253-260.
    View publication on PubMed
Search for more literature for 6.5.1.2

Cloned(Commentary)

Cloned (Comment) Organism
full length and truncated enzymes expressed in Escherichia coli BL21 (DE3) Aquifex pyrophilus

Protein Variants

Protein Variants Comment Organism
DELTA1-525 no DNA-binding Aquifex pyrophilus
DELTA1-90 very low self adenylation activity, active in DNA-ligation, reduced DNA-binding Aquifex pyrophilus
DELTA1-90,363-719 no self adenylation Aquifex pyrophilus
DELTA1-90,487-719 very low self adenylation activity Aquifex pyrophilus
DELTA363-719 full self adenylation activity Aquifex pyrophilus
DELTA517-719 full self adenylation activity Aquifex pyrophilus
DELTA636-719 active in DNA-ligation Aquifex pyrophilus

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ zinc binding motif, Cys437, Cys440, Cys455, Cys460 Aquifex pyrophilus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m Aquifex pyrophilus 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
Aquifex pyrophilus
-
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant proteins Aquifex pyrophilus

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 Aquifex pyrophilus
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Aquifex pyrophilus 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 Aquifex pyrophilus AMP + nicotinamide nucleotide + (deoxyribonucleotide)n+m
-
 ?

Cofactor

Cofactor Comment Organism Structure
NAD+ required Aquifex pyrophilus