BRENDA - Enzyme Database

Structural elements in IGP synthase exclude water to optimize ammonia transfer

Amaro, R.E.; Myers, R.S.; Davisson, V.J.; Luthey-Schulten, Z.A.; Biophys. J. 89, 475-487 (2005)

Data extracted from this reference:

Engineering
EC Number
Protein Variants
Commentary
Organism
4.3.2.10
K360A
formation of a larger opening between chamber I and chamber II, mutation results in a threefold decrease in the overall reaction stoichiometry. Although the mutation facilitates the passage of ammonia into the channel, without the lysine side chain the ammonia diffuses more easily around the interface
Saccharomyces cerevisiae
4.3.2.10
R239A
the mutation creates a large hole in the exposed side of the interface, the mutation results in a 1000 decrease in kcat/Km values for the cyclase reaction, the mutation allows bulk water molecules to penetrate chamber II, thereby disrupting the passage of ammonia and destroying the tightly coupled reaction kinetics
Saccharomyces cerevisiae
4.3.2.10
Y144F
no loss in protein function occurrs with the Y138F mutation. This indicates that the main function of this residue is to prevent bulk water from entering the interface during the reaction and keep ammonia sequestered within the intermolecular channel
Saccharomyces cerevisiae
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.3.2.10
additional information
-
L-glutamine
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
4.3.2.10
additional information
-
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
Saccharomyces cerevisiae
the enzyme participates in the pathway of histidine biosynthesis
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
Saccharomyces cerevisiae ATCC 204508
the enzyme participates in the pathway of histidine biosynthesis
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
?
Organism
EC Number
Organism
UniProt
Commentary
Textmining
4.3.2.10
Saccharomyces cerevisiae
P33734
-
-
4.3.2.10
Saccharomyces cerevisiae ATCC 204508
P33734
-
-
Purification (Commentary)
EC Number
Purification (Commentary)
Organism
4.3.2.10
His-tagged IGP synthase
Saccharomyces cerevisiae
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the enzyme participates in the pathway of histidine biosynthesis
747285
Saccharomyces cerevisiae
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the first domain of IGP synthase, a triad glutamine amidotransferase, hydrolyzes glutamine to form glutamate and ammonia. Its activity is tightly regulated by the binding of the substrate 5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide to its partner synthase domain. Structural elements in IGP synthase exclude water to optimize ammonia transfer
747285
Saccharomyces cerevisiae
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the enzyme participates in the pathway of histidine biosynthesis
747285
Saccharomyces cerevisiae ATCC 204508
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the first domain of IGP synthase, a triad glutamine amidotransferase, hydrolyzes glutamine to form glutamate and ammonia. Its activity is tightly regulated by the binding of the substrate 5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide to its partner synthase domain. Structural elements in IGP synthase exclude water to optimize ammonia transfer
747285
Saccharomyces cerevisiae ATCC 204508
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + NH4+
-
747285
Saccharomyces cerevisiae
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H2O
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + NH4+
-
747285
Saccharomyces cerevisiae ATCC 204508
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H2O
-
-
-
?
Synonyms
EC Number
Synonyms
Commentary
Organism
4.3.2.10
IGP synthase
-
Saccharomyces cerevisiae
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.3.2.10
additional information
-
L-glutamine
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
4.3.2.10
additional information
-
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.3.2.10
7
-
assay at
Saccharomyces cerevisiae
Engineering (protein specific)
EC Number
Protein Variants
Commentary
Organism
4.3.2.10
K360A
formation of a larger opening between chamber I and chamber II, mutation results in a threefold decrease in the overall reaction stoichiometry. Although the mutation facilitates the passage of ammonia into the channel, without the lysine side chain the ammonia diffuses more easily around the interface
Saccharomyces cerevisiae
4.3.2.10
R239A
the mutation creates a large hole in the exposed side of the interface, the mutation results in a 1000 decrease in kcat/Km values for the cyclase reaction, the mutation allows bulk water molecules to penetrate chamber II, thereby disrupting the passage of ammonia and destroying the tightly coupled reaction kinetics
Saccharomyces cerevisiae
4.3.2.10
Y144F
no loss in protein function occurrs with the Y138F mutation. This indicates that the main function of this residue is to prevent bulk water from entering the interface during the reaction and keep ammonia sequestered within the intermolecular channel
Saccharomyces cerevisiae
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.3.2.10
additional information
-
L-glutamine
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
4.3.2.10
additional information
-
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
Saccharomyces cerevisiae
the enzyme participates in the pathway of histidine biosynthesis
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
Saccharomyces cerevisiae ATCC 204508
the enzyme participates in the pathway of histidine biosynthesis
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.2.10
His-tagged IGP synthase
Saccharomyces cerevisiae
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the enzyme participates in the pathway of histidine biosynthesis
747285
Saccharomyces cerevisiae
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the first domain of IGP synthase, a triad glutamine amidotransferase, hydrolyzes glutamine to form glutamate and ammonia. Its activity is tightly regulated by the binding of the substrate 5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide to its partner synthase domain. Structural elements in IGP synthase exclude water to optimize ammonia transfer
747285
Saccharomyces cerevisiae
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the enzyme participates in the pathway of histidine biosynthesis
747285
Saccharomyces cerevisiae ATCC 204508
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine
the first domain of IGP synthase, a triad glutamine amidotransferase, hydrolyzes glutamine to form glutamate and ammonia. Its activity is tightly regulated by the binding of the substrate 5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide to its partner synthase domain. Structural elements in IGP synthase exclude water to optimize ammonia transfer
747285
Saccharomyces cerevisiae ATCC 204508
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + L-glutamate
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + NH4+
-
747285
Saccharomyces cerevisiae
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H2O
-
-
-
?
4.3.2.10
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + NH4+
-
747285
Saccharomyces cerevisiae ATCC 204508
5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H2O
-
-
-
?
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.3.2.10
additional information
-
L-glutamine
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
4.3.2.10
additional information
-
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.3.2.10
7
-
assay at
Saccharomyces cerevisiae
General Information
EC Number
General Information
Commentary
Organism
4.3.2.10
metabolism
the enzyme participates in the pathway of histidine biosynthesis
Saccharomyces cerevisiae
General Information (protein specific)
EC Number
General Information
Commentary
Organism
4.3.2.10
metabolism
the enzyme participates in the pathway of histidine biosynthesis
Saccharomyces cerevisiae
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
4.3.2.10
additional information
-
L-glutamine
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
4.3.2.10
additional information
-
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
4.3.2.10
additional information
-
L-glutamine
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae
4.3.2.10
additional information
-
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
pH 7.0, 25°C, kinetic constants are determined for wild-type and mutant enzymes
Saccharomyces cerevisiae