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Literature summary for 6.5.1.1 extracted from

  • Williamson, A.; Rothweiler, U.; Leiros, H.K.
    Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface (2014), Acta Crystallogr. Sect. D, 70, 3043-3056 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 6.5.1.1

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3)Star cells Psychromonas sp. SP041

Crystallization (Commentary)

Crystallization (Comment) Organism
hanging drop vapor diffusion method, using 0.1 M HEPES pH 7.4, 1.6-1.9 M ammonium sulfate Psychromonas sp. SP041

Inhibitors

Inhibitors Comment Organism Structure
additional information no inhibition with ATP concentrations up to 0.5 mM Psychromonas sp. SP041
NaCl NaCl concentrations above 100 mM have an inhibitory effect Psychromonas sp. SP041

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.000124
-
 (nicked double-stranded DNA)n at 30°C, pH not specified in the publication Psychromonas sp. SP041
0.0038
-
 ATP at 30°C, pH not specified in the publication Psychromonas sp. SP041

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ MgCl2 is required for enzyme activity, with an optimal concentration between 1 and 5 mM Psychromonas sp. SP041

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m Psychromonas sp. SP041
-
 (deoxyribonucleotide)n+m + AMP + diphosphate
-
 ?
ATP + [DNA ligase]-L-lysine Psychromonas sp. SP041
-
 [DNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
-
 ?

Organism

Organism UniProt Comment Textmining
Psychromonas sp. SP041 A0A0A6YVN6
-
-

Purification (Commentary)

Purification (Comment) Organism
-
 Psychromonas sp. SP041

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m
-
 Psychromonas sp. SP041 (deoxyribonucleotide)n+m + AMP + diphosphate
-
 ?
ATP + (nicked double-stranded DNA)n + (nicked double-stranded DNA)m
-
 Psychromonas sp. SP041 AMP + diphosphate + (nicked double-stranded DNA)n+m
-
 ?
ATP + [DNA ligase]-L-lysine
-
 Psychromonas sp. SP041 [DNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
-
 ?
additional information in addition to sealing a singly nicked fully matched double-stranded DNA substrate, the enzyme is also able to ligate a cohesive-ended double-stranded break and a single nick with a 1 base pair mismatch at the 3'-OH position of the nick, albeit with reduced efficiency. Ligation of a blunt-end double-stranded break and a 1 nucleotide gapped substrate is also detected when enzyme concentrations and extended incubation times are used; however, no activity is seen with a nonphosphorylated 5'-nicked strand or single-stranded DNA Psychromonas sp. SP041 ?
-
 ?

Synonyms

Synonyms Comment Organism
ADL
-
 Psychromonas sp. SP041
ATP-dependent DNA ligase
-
 Psychromonas sp. SP041

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.05
-
 (nicked double-stranded DNA)n at 30°C, pH not specified in the publication Psychromonas sp. SP041