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Literature summary for 6.5.1.1 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)

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

Protein Variants

Protein Variants Comment Organism
A576P the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum
D162E the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum
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
N255G the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum
T491S the mutation hardly affects ligation activity at pH 3.0 Ferroplasma acidiphilum

Metals/Ions

Metals/Ions Comment Organism Structure
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
additional information catalytic activity neither depends on nor is stimulated by added Mg2+ or K+ Ferroplasma acidiphilum

Organism

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

Purification (Commentary)

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

Substrates and Products (Substrate)

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

Synonyms

Synonyms Comment Organism
DNA ligase
-
Ferroplasma acidiphilum
Lig
-
Ferroplasma acidiphilum

Turnover Number [1/s]

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

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
1.5 3 pH-optimum in vitro Ferroplasma acidiphilum
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

pH Minimum pH Maximum Comment Organism
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

pH Stability pH Stability Maximum Comment Organism
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

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