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Literature summary extracted from

  • Ferrer, M.; Golyshina, O.V.; Beloqui, A.; Boettger, L.H.; Andreu, J.M.; Polaina, J.; De Lacey, A.L.; Trautwein, A.X.; Timmis, K.N.; Golyshin, P.N.
    A purple acidophilic di-ferric DNA ligase from Ferroplasma (2008), Proc. Natl. Acad. Sci. USA, 105, 8878-8883.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
6.5.1.1 expressed in Escherichia coli strain ORIGAMI(DE3)pLysS Ferroplasma acidiphilum

Protein Variants

EC Number Protein Variants Comment Organism
6.5.1.1 A576P the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum
6.5.1.1 D162E the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum
6.5.1.1 E134L the mutation causes a 60% reduction at pH 3.0, with no net change in iron content and purple color, the mutant has an activity optimum of pH 5.0 and a 1.5fold higher turnover number as the wild type enzyme Ferroplasma acidiphilum
6.5.1.1 N255G the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum
6.5.1.1 T491S the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
6.5.1.1 Fe3+ contains two Fe3+-tyrosinate centers, reduction of the Fe3+ to Fe2+ results in an 80% decrease in DNA substrate binding and an increase in the pH activity optimum to 5.0 Ferroplasma acidiphilum
6.5.1.1 additional information catalytic activity neither depends on nor is stimulated by added Mg2+ or K+ Ferroplasma acidiphilum

Organism

EC Number Organism UniProt Comment Textmining
6.5.1.1 Ferroplasma acidiphilum Q2PCE4
-
-
6.5.1.1 Ferroplasma acidiphilum YT / DSM 12658 Q2PCE4
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
6.5.1.1 Resource Q column chromatography and Superdex-200 gel filtration Ferroplasma acidiphilum

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Ferroplasma acidiphilum AMP + diphosphate + (deoxyribonucleotide)m+n
-
 ?
6.5.1.1 ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
-
 Ferroplasma acidiphilum YT / DSM 12658 AMP + diphosphate + (deoxyribonucleotide)m+n
-
 ?

Synonyms

EC Number Synonyms Comment Organism
6.5.1.1 DNA ligase
-
 Ferroplasma acidiphilum
6.5.1.1 Lig
-
 Ferroplasma acidiphilum

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
6.5.1.1 0.025
-
 (deoxyribonucleotide)n mutant enzyme E143L Ferroplasma acidiphilum
6.5.1.1 0.048
-
 (deoxyribonucleotide)n mutant enzyme T491S Ferroplasma acidiphilum
6.5.1.1 0.05
-
 (deoxyribonucleotide)n mutant enzyme D162E Ferroplasma acidiphilum
6.5.1.1 0.051
-
 (deoxyribonucleotide)n mutant enzyme A576P Ferroplasma acidiphilum
6.5.1.1 0.051
-
 (deoxyribonucleotide)n mutant enzyme N255G Ferroplasma acidiphilum
6.5.1.1 0.056
-
 (deoxyribonucleotide)n wild type enzyme Ferroplasma acidiphilum

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.5.1.1 1.5 3 pH-optimum in vitro Ferroplasma acidiphilum
6.5.1.1 5
-
 reduction of the Fe3+ to Fe2+ results in an 80% decrease in DNA substrate binding and an increase in the pH activity optimum to 5.0 Ferroplasma acidiphilum

pH Range

EC Number pH Minimum pH Maximum Comment Organism
6.5.1.1 1.5 5 ligation activities, at 40°C under conditions of substrate saturation, are highest at pH 2.5-3.0, only slightly lower at pH 1.5-2.0 (about 80%) and are practically undetectable above pH 5.0 Ferroplasma acidiphilum

pH Stability

EC Number pH Stability pH Stability Maximum Comment Organism
6.5.1.1 2 3 LigFa is acid-tolerant and retains about 95% of its activity after incubation at pH 2.0-3.0 for 10 h but is unstable at higher pH levels Ferroplasma acidiphilum

Cofactor

EC Number Cofactor Comment Organism Structure
6.5.1.1 ATP ATP is preferred over NAD+ Ferroplasma acidiphilum
6.5.1.1 NAD+ uses also NAD+ as cofactor although ATP is preferred Ferroplasma acidiphilum