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Literature summary extracted from

  • Miyamoto, Y.; Masaki, T.; Chohnan, S.
    Characterization of N-deoxyribosyltransferase from Lactococcus lactis subsp. lactis (2007), Biochim. Biophys. Acta, 1774, 1323-1330.
    View publication on PubMed

Activating Compound

EC Number Activating Compound Comment Organism Structure
2.4.2.6 K+ K+-activated type II enzyme: binding of K+ is required to enhance activity through induced conformational change Lactococcus lactis
2.4.2.6 additional information does not require phosphate derivatives such as ATP, thiamine diphosphate, pyridoxal phosphate to complete 2-deoxyribose transfer Lactococcus lactis

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.4.2.6 in pET-22b(+) for expression in Escherichia coli BL21(DE3) Lactococcus lactis
2.4.2.6 in pGEM-T for cloning Lactococcus lactis

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.4.2.6 Ca2+ inhibits base exchange activity at 1 mM Lactococcus lactis
2.4.2.6 CO2 reduces base exchange activity by 87-99% at 1 mM Lactococcus lactis
2.4.2.6 Cu2+ reduces base exchange activity by 87-99% at 1 mM Lactococcus lactis
2.4.2.6 Mg2+ inhibits base exchange activity at 1mM Lactococcus lactis
2.4.2.6 Mn2+ reduces base exchange activity by 87-99% at 1 mM Lactococcus lactis
2.4.2.6 Zn2+ reduces base exchange activity by 87-99% at 1 mM Lactococcus lactis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.4.2.6 K+ enhances base exchange activity and thermostability, 1.66-fold activation by 1 mM KCl (reaches plateau at 20 mM) Lactococcus lactis
2.4.2.6 additional information enzymatic activity depends on monovalent cations as cofactors rather than catalysts Lactococcus lactis
2.4.2.6 additional information K+ and NH4+ have no synergistic effects Lactococcus lactis
2.4.2.6 additional information Li+ and Na+ do not activate Lactococcus lactis
2.4.2.6 NH4+ enhances base exchange activity and thermostability, 1.43-fold activation by 1 mM (NH4)2SO4 (reaches plateau at 20 mM) Lactococcus lactis
2.4.2.6 Rb+ enhances base exchange activity, 1.51-fold activation by 1 mM RbCl Lactococcus lactis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
2.4.2.6 17250
-
4 * 17250, elution as single peak from the preparative gel filtration column Lactococcus lactis
2.4.2.6 18290
-
theoretical molecular weight Lactococcus lactis
2.4.2.6 25500
-
according to migration in SDS-12.5% polyacrylamide gel electrophoresis Lactococcus lactis
2.4.2.6 69000
-
gel filtration chromatography Lactococcus lactis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.4.2.6 additional information Lactococcus lactis preferably purine 2-deoxyribonucleoside synthesis compared to pyrimidine deoxyribonucleoside synthesis although both are catalysed ?
-
?
2.4.2.6 purine base + 2-deoxy-D-ribosyl-base Lactococcus lactis
-
purine deoxyribonucleoside + base preferred over pyrimidine deoxyribonucleoside synthesis r
2.4.2.6 pyrimidine base + 2-deoxy-D-ribosyl-base Lactococcus lactis
-
pyrimidine deoxyribonucleoside + base
-
r

Organism

EC Number Organism UniProt Comment Textmining
2.4.2.6 Lactococcus lactis
-
subsp. lactis JCM5808
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.4.2.6 preclearing of bacterial lysate with 40% ammonium sulfate and subsequent precipitation of proteins with 90% ammonium sulfate, gel filtration of dissolved protein on Sephacryl S-200 column, combination of fractions with N-deoxyribosyltransferase activity, precipitation of proteins with 90% ammonium sulfate, dialysis of dissolved proteins and concentration by ultrafiltration, second gel filtration on Sephacryl S-200 column, combination of active fractions and concentration by ultrafiltration, recovery of 70.4% of activity, storage at -20°C in 50% glycerol Lactococcus lactis

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
2.4.2.6 additional information
-
0.9% in presence of 1 mM ZnCl2 Lactococcus lactis
2.4.2.6 additional information
-
102% in presence of 1 mM NaCl Lactococcus lactis
2.4.2.6 additional information
-
105% in presence of 1 mM CsCl Lactococcus lactis
2.4.2.6 additional information
-
106% in presence of 1 mM NaSO4 Lactococcus lactis
2.4.2.6 additional information
-
12.9% in presence of 1 mM CoCl2 Lactococcus lactis
2.4.2.6 additional information
-
143% in presence of 1 mM NH4Cl Lactococcus lactis
2.4.2.6 additional information
-
151% in presence of 1 mM RbCl Lactococcus lactis
2.4.2.6 additional information
-
163% in presence of 1 mM (NH4)2SO4 Lactococcus lactis
2.4.2.6 additional information
-
165% in presence of 1 mM K2SO4 Lactococcus lactis
2.4.2.6 additional information
-
166% in presence of 1 mM (NH4)2SO4 and 1 mM KCl Lactococcus lactis
2.4.2.6 additional information
-
166% in presence of 1 mM KCl Lactococcus lactis
2.4.2.6 additional information
-
192% in presence of 10 mM KCl Lactococcus lactis
2.4.2.6 additional information
-
194% in presence of 10 mM (NH4)2SO4 Lactococcus lactis
2.4.2.6 additional information
-
3.2% in presence of 1 mM CuSO4 Lactococcus lactis
2.4.2.6 additional information
-
51.8% in presence of 1 mM CaCl2 Lactococcus lactis
2.4.2.6 additional information
-
66.3% in presence of 1 mM MgCl2 Lactococcus lactis
2.4.2.6 additional information
-
66% in presence of 1 mM MgSO4 Lactococcus lactis
2.4.2.6 additional information
-
68.3% in presence of 1 mM FeCl2 Lactococcus lactis
2.4.2.6 additional information
-
97.7% in presence of 1 mM LiCl Lactococcus lactis
2.4.2.6 6.67
-
equals 100%, purified protein, in presence of 0.5 mg/ml bovine serum albumin, pH 7.5, 10 min, 25°C Lactococcus lactis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.4.2.6 adenine + deoxycytidine 64.0% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyadenosine + cytosine
-
r
2.4.2.6 adenine + deoxyguanosine 46.6% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyadenosine + guanine
-
r
2.4.2.6 adenine + deoxyinosine 57.3% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyadenosine + hypoxanthine
-
r
2.4.2.6 adenine + deoxyuridine 75.4% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyadenosine + uracil
-
r
2.4.2.6 adenine + thymidine 74.6% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyadenosine + thymine
-
r
2.4.2.6 cytosine + deoxyadenosine 27.7% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxycytidine + adenine
-
r
2.4.2.6 cytosine + deoxyguanosine 25.7% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxycytidine + guanine
-
r
2.4.2.6 cytosine + deoxyinosine 32.0% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxycytidine + hypoxanthine
-
r
2.4.2.6 cytosine + deoxyuridine 62.9% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxycytidine + uracil
-
r
2.4.2.6 cytosine + thymidine 53.5% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxycytidine + thymine
-
r
2.4.2.6 cytosine + thymidine standard reaction for cofactor analyses as well as activating compound and inhibitor studies, in presence of 40 mM ammonium sulfate and 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxycytidine + thymine
-
r
2.4.2.6 hypoxanthine + deoxyadenosine 38.0% conversion after 4 h at standard reaction conditions: 2 mM substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyinosine + adenine
-
r
2.4.2.6 hypoxanthine + deoxycytidine 51.9% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyinosine + cytosine
-
r
2.4.2.6 hypoxanthine + deoxyguanosine 25.2% conversion after 4 h at standard reaction conditions: 2 mM substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyinosine + guanine
-
r
2.4.2.6 hypoxanthine + deoxyuridine 65.6% conversion after 4 h at standard reaction conditions: 2 mM substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyinosine + uracil
-
r
2.4.2.6 hypoxanthine + thymidine 76.8% conversion after 4 h at standard reaction conditions: 2 mM substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyinosine + thymine
-
r
2.4.2.6 additional information preferably purine 2-deoxyribonucleoside synthesis compared to pyrimidine deoxyribonucleoside synthesis although both are catalysed Lactococcus lactis ?
-
?
2.4.2.6 additional information ribonucleoside, arabinosylnucleoside and 2,3-dideoxyribonucleoside are no substrates for base-exchange by YejD Lactococcus lactis ?
-
?
2.4.2.6 purine base + 2-deoxy-D-ribosyl-base
-
Lactococcus lactis purine deoxyribonucleoside + base preferred over pyrimidine deoxyribonucleoside synthesis r
2.4.2.6 pyrimidine base + 2-deoxy-D-ribosyl-base
-
Lactococcus lactis pyrimidine deoxyribonucleoside + base
-
r
2.4.2.6 thymine + deoxyadenosine 22.7% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis thymidine + adenine
-
r
2.4.2.6 thymine + deoxycytidine 38.3% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis thymidine + cytosine
-
r
2.4.2.6 thymine + deoxyguanosine 17.7% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis thymidine + guanine
-
r
2.4.2.6 thymine + deoxyinosine 19.5% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin, equilibrium reached after 2 h Lactococcus lactis thymidine + hypoxanthine
-
r
2.4.2.6 thymine + deoxyuridine 53.7% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis thymidine + uracil
-
r
2.4.2.6 uracil + deoxyadenosine 17.1% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyuridine + adenine
-
r
2.4.2.6 uracil + deoxycytidine 37.7% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyuridine + cytosine
-
r
2.4.2.6 uracil + deoxyguanosine 16.1% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyuridine + guanine
-
r
2.4.2.6 uracil + deoxyinosine 23.8% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyuridine + hypoxanthine
-
r
2.4.2.6 uracil + thymidine 43.0% conversion after 4 h at standard reaction conditions: 2 mM each substrate, 0.013 U NTD, pH 7.5, 25°C, 40 mM (NH4)2SO4, 0.5 mg/ml bovine serum albumin Lactococcus lactis deoxyuridine + thymine
-
r

Subunits

EC Number Subunits Comment Organism
2.4.2.6 homotetramer 4 * 17250, elution as single peak from the preparative gel filtration column Lactococcus lactis

Synonyms

EC Number Synonyms Comment Organism
2.4.2.6 N-deoxyribosyltransferase
-
Lactococcus lactis
2.4.2.6 NTD
-
Lactococcus lactis
2.4.2.6 nucleoside N-deoxyribosyltransferase
-
Lactococcus lactis
2.4.2.6 trans-N-deoxyribosylase
-
Lactococcus lactis
2.4.2.6 YejD
-
Lactococcus lactis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.4.2.6 30
-
assay at, pH 7.5 Lactococcus lactis

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
2.4.2.6 additional information
-
(NH4)2SO4 is more thermostabilizing than KCl Lactococcus lactis
2.4.2.6 25
-
pH 7.5, 20 min, 60% activity lost, in presence of 10 mM (NH4)2SO4 only 20% activity lost, in presence of 500 mM KCL only 6% activity lost Lactococcus lactis
2.4.2.6 30
-
pH 7.5, 20 min, in presence of 500 mM (NH4)2SO4 fully active Lactococcus lactis
2.4.2.6 35
-
and more, pH 7.5, 20 min, 75% activity lost Lactococcus lactis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.4.2.6 7.5
-
assay at Lactococcus lactis