An iron(II) dependent formamide hydrolase catalyzes the second step in the archaeal biosynthetic pathway to riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin
Grochowski, L.L.; Xu, H.; White, R.H.; Biochemistry 48, 4181-4188 (2009) 
Data extracted from this reference:
Activating Compound
Activating Compound
Commentary
Organism
Structure
dithiothreitol
ArfB is not active in the absence of 2 mM dithiothreitol
Methanocaldococcus jannaschii
Cloned(Commentary)
Cloned (Commentary)
Organism
in Escherichia coli
Methanocaldococcus jannaschii
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1
-
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate
pH 7.2, 70°C, apparent Km-value is about 1 mM at a concentration of 2 mM Fe2+, type of curve is typically indicative of homomeric cooperativity and suggests that ArfB may exhibit positive cooperative substrate binding
Methanocaldococcus jannaschii
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
addition of more than 1 mM Fe2+ increases the rate of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate production by more than 10fold, purified enzyme contains both 1.4 mol iron and 6.2 mol magnesium per mol of protomer, maximum activity of Chelex-treated enzyme with added Fe2+ is 30% that of the untreated enzyme indicating that the apoenzyme cannot be fully reconstituted with the addition of just one metal
Methanocaldococcus jannaschii
Mg2+
enzyme contains both 1.4 mol Fe2+ and 6.2 mol Mg2+ per mol of protomer
Methanocaldococcus jannaschii
Mn2+
addition of more than 1 mM Mn2+ increases the rate of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate production by more than 10fold, maximum activity of Chelex-treated enzyme with added Mn2+ is 30% that of the untreated enzyme indicating that the apoenzyme cannot be fully reconstituted with the addition of just one metal
Methanocaldococcus jannaschii
Zn2+
zinc is associated with the purified protein, 1.5 mol/protomer, despite the presence of zinc in the protein, addition of Zn(II) to the incubation mixture containing purified enzyme or apo-enzyme does not activate ArfB
Methanocaldococcus jannaschii
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
25000
-
2 * 25000
Methanocaldococcus jannaschii
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + H2O
Methanocaldococcus jannaschii
enzyme catalyzes the second step in archaeal riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin biosynthesis. The archaeal pathway begins with an archaeal-specific GTP cyclohydrolase IIa (EC 3.5.4.29) that hydrolyzes the imidazole ring of GTP. The bacterial enzyme, EC 3.5.4.25 (GTP cyclohydrolase II) catalyzes both reactions
2,5-diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Methanocaldococcus jannaschii
Q57580
-
-
Purification (Commentary)
Purification (Commentary)
Organism
purified by anion-exchange chromatography
Methanocaldococcus jannaschii
Specific Activity [micromol/min/mg]
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
6
-
Vmax at a concentration of 2 mM Fe2+, 5 mM MgCl2, 10 mM dithiothreitol and 25 mM TES, pH 7.2
Methanocaldococcus jannaschii
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + H2O
-
696333
Methanocaldococcus jannaschii
2,5-diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate
-
-
-
?
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + H2O
enzyme catalyzes the second step in archaeal riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin biosynthesis. The archaeal pathway begins with an archaeal-specific GTP cyclohydrolase IIa (EC 3.5.4.29) that hydrolyzes the imidazole ring of GTP. The bacterial enzyme, EC 3.5.4.25 (GTP cyclohydrolase II) catalyzes both reactions
696333
Methanocaldococcus jannaschii
2,5-diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate
-
-
-
?
Subunits
Subunits
Commentary
Organism
dimer
2 * 25000
Methanocaldococcus jannaschii
Synonyms
Synonyms
Commentary
Organism
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-monophosphate deformylase
-
Methanocaldococcus jannaschii
ArfB
-
Methanocaldococcus jannaschii
MJ0116
-
Methanocaldococcus jannaschii
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
70
-
assay at
Methanocaldococcus jannaschii
Temperature Stability [°C]
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
80
-
stable at
Methanocaldococcus jannaschii
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.2
-
assay at
Methanocaldococcus jannaschii
pH Range
pH Minimum
pH Maximum
Commentary
Organism
6.5
8.5
pH 6.5: about 80% of maximal activity, pH 8.5: about 40% of maximal activity
Methanocaldococcus jannaschii
Activating Compound (protein specific)
Activating Compound
Commentary
Organism
Structure
dithiothreitol
ArfB is not active in the absence of 2 mM dithiothreitol
Methanocaldococcus jannaschii
Cloned(Commentary) (protein specific)
Commentary
Organism
in Escherichia coli
Methanocaldococcus jannaschii
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1
-
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate
pH 7.2, 70°C, apparent Km-value is about 1 mM at a concentration of 2 mM Fe2+, type of curve is typically indicative of homomeric cooperativity and suggests that ArfB may exhibit positive cooperative substrate binding
Methanocaldococcus jannaschii
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
addition of more than 1 mM Fe2+ increases the rate of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate production by more than 10fold, purified enzyme contains both 1.4 mol iron and 6.2 mol magnesium per mol of protomer, maximum activity of Chelex-treated enzyme with added Fe2+ is 30% that of the untreated enzyme indicating that the apoenzyme cannot be fully reconstituted with the addition of just one metal
Methanocaldococcus jannaschii
Mg2+
enzyme contains both 1.4 mol Fe2+ and 6.2 mol Mg2+ per mol of protomer
Methanocaldococcus jannaschii
Mn2+
addition of more than 1 mM Mn2+ increases the rate of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate production by more than 10fold, maximum activity of Chelex-treated enzyme with added Mn2+ is 30% that of the untreated enzyme indicating that the apoenzyme cannot be fully reconstituted with the addition of just one metal
Methanocaldococcus jannaschii
Zn2+
zinc is associated with the purified protein, 1.5 mol/protomer, despite the presence of zinc in the protein, addition of Zn(II) to the incubation mixture containing purified enzyme or apo-enzyme does not activate ArfB
Methanocaldococcus jannaschii
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
25000
-
2 * 25000
Methanocaldococcus jannaschii
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + H2O
Methanocaldococcus jannaschii
enzyme catalyzes the second step in archaeal riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin biosynthesis. The archaeal pathway begins with an archaeal-specific GTP cyclohydrolase IIa (EC 3.5.4.29) that hydrolyzes the imidazole ring of GTP. The bacterial enzyme, EC 3.5.4.25 (GTP cyclohydrolase II) catalyzes both reactions
2,5-diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
purified by anion-exchange chromatography
Methanocaldococcus jannaschii
Specific Activity [micromol/min/mg] (protein specific)
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
6
-
Vmax at a concentration of 2 mM Fe2+, 5 mM MgCl2, 10 mM dithiothreitol and 25 mM TES, pH 7.2
Methanocaldococcus jannaschii
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + H2O
-
696333
Methanocaldococcus jannaschii
2,5-diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate
-
-
-
?
2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + H2O
enzyme catalyzes the second step in archaeal riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin biosynthesis. The archaeal pathway begins with an archaeal-specific GTP cyclohydrolase IIa (EC 3.5.4.29) that hydrolyzes the imidazole ring of GTP. The bacterial enzyme, EC 3.5.4.25 (GTP cyclohydrolase II) catalyzes both reactions
696333
Methanocaldococcus jannaschii
2,5-diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
2 * 25000
Methanocaldococcus jannaschii
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
70
-
assay at
Methanocaldococcus jannaschii
Temperature Stability [°C] (protein specific)
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
80
-
stable at
Methanocaldococcus jannaschii
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.2
-
assay at
Methanocaldococcus jannaschii
pH Range (protein specific)
pH Minimum
pH Maximum
Commentary
Organism
6.5
8.5
pH 6.5: about 80% of maximal activity, pH 8.5: about 40% of maximal activity
Methanocaldococcus jannaschii
Other publictions for EC 3.5.1.102
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
696333
Grochowski
An iron(II) dependent formamid ...
Methanocaldococcus jannaschii
Biochemistry
48
4181-4188
2009
1
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1
-
-
-
-
1
-
4
1
1
-
4
-
-
1
-
-
-
1
-
2
1
3
1
-
1
-
1
1
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
1
-
4
1
1
-
-
-
1
-
-
1
-
2
1
1
-
1
-
1
1
-
-
-
-
-
-
-
-