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Enzyme Nomenclature
Information on EC 1.7.1.13 - preQ1 synthase
for references in articles please use BRENDA:EC1.7.1.13
Word Map on EC 1.7.1.13
- 1.7.1.13
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queuosine
- nucleoside
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imine
- gtp
- subtilis
- 7-aminomethyl-7-deazaguanine
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
1.7.1.13
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RECOMMENDED NAME
GeneOntology No.
preQ1 synthase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
7-aminomethyl-7-carbaguanine + 2 NADP+ = 7-cyano-7-carbaguanine + 2 NADPH + 2 H+
This enzyme catalyses one of the early steps in the synthesis of queosine (Q-tRNA), and is followed by the action of EC 2.4.2.29, queuine tRNA-ribosyltransferase. Queosine is found in the wobble position of tRNAGUN in Eukarya and Bacteria [2] and is thought to be involved in translational modulation. The enzyme is not a GTP cyclohydrolase, as was thought previously based on sequence-homology studies.
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
7-aminomethyl-7-carbaguanine:NADP+ oxidoreductase
The reaction occurs in the reverse direction. This enzyme catalyses one of the early steps in the synthesis of queuosine (Q-tRNA), and is followed by the action of EC 2.4.2.29, queuine tRNA-ribosyltransferase. Queuosine is found in the wobble position of tRNAGUN in Eukarya and Bacteria [2] and is thought to be involved in translational modulation. The enzyme is not a GTP cyclohydrolase, as was thought previously based on sequence-homology studies.
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one + 2 NADPH + 2 H+
2-amino-5-amino-methyl-pyrrolo[2,3-d]pyrimidin-4-one + 2 NADP+
natural substrate
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?
2-amino-5-cyanopyrrolo[2,3-d]pyrimidine + 2 NADPH + 2 H+
2-amino-5-amino-methyl-pyrrolo[2,3-d]pyrimidine + 2 NADP+
analogue of natural substrate, poor substrate
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?
5-cyanopyrrolo[2,3-d]pyrimidin-4-one + 2 NADPH + 2 H+
5-amino-methyl-pyrrolo[2,3-d]pyrimidin-4-one + 2 NADP+
analogue of natural substrate
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?
7-cyano-7-carba-2-deaminoguanine + 2 NADPH + 2 H+
7-aminomethyl-7-carba-2-deaminoguanine + 2 NADP+
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?
7-cyano-7-carbaguanine + 2 NADPH + 2 H+
7-aminomethyl-7-carbaguanine + 2 NADP+
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?
7-cyano-7-carbaguanine + 2 NADPH + 2 H+
7-aminomethyl-7-carbaguanine + 2 NADP+
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?
7-cyano-7-carbaguanine + 2 NADPH + 2 H+
7-aminomethyl-7-carbaguanine + 2 NADP+
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?
7-cyano-7-carbaguanine + 2 NADPH + 2 H+
7-aminomethyl-7-carbaguanine + 2 NADP+
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?
7-cyano-7-carbaguanine + 2 NADPH + 2 H+
7-aminomethyl-7-carbaguanine + 2 NADP+
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
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late step in biosynthesis of the modified tRNA nucleoside queuosine
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
late step in biosynthesis of the modified tRNA nucleoside queuosine
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
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late step in biosynthesis of the modified tRNA nucleoside queuosine
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
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queuine is 7-aminomethyl-7-deazaguanine
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
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queuine is 7-aminomethyl-7-deazaguanine
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?
additional information
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no substrates: acetonitrile, benzonitrile and benzylcyanide
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additional information
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during catalysis each active site of the dimeric enzyme binds one substrate molecule. NADPH binds independent of the substrate. The PreQ0 binding pocket of the active site is not involved in the binding of NADPH
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additional information
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QueF binds substrate preQ0 in a strongly exothermic process (DeltaH 80.3 kJ/mol) whereby the thioimide adduct is formed with half-of-the-sites reactivity in the homodimeric enzyme. Both steps of preQ0 reduction involve transfer of the 4-pro-R-hydrogen from NADPH. They proceed about 4-7fold more slowly than trapping of the enzyme-bound preQ0 as covalent thioimide and are mainly rate-limiting for the enzyme's kcat
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additional information
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enzyme is highly specific for substrate preQ0
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additional information
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enzyme is highly specific for substrate preQ0
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additional information
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the nitrile to amine conversion proceeds through four major stages: formation of a C-S covalent bond between the substrate and the catalytic cysteine residue to form the thioimidate intermediate, hydride transfer from NADPH to the substrate to generate the thiohemiaminal intermediate, cleavage of the C-S covalent bond to generate the imine intermediate, and second hydride transfer from NADPH to the imine intermediate to generate the final amine product. The free energy barrier for the rate-limiting step, i.e. the second hydride transfer, is20.8 kcal/mol
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additional information
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the nitrile to amine conversion proceeds through four major stages: formation of a C-S covalent bond between the substrate and the catalytic cysteine residue to form the thioimidate intermediate, hydride transfer from NADPH to the substrate to generate the thiohemiaminal intermediate, cleavage of the C-S covalent bond to generate the imine intermediate, and second hydride transfer from NADPH to the imine intermediate to generate the final amine product. The free energy barrier for the rate-limiting step, i.e. the second hydride transfer, is20.8 kcal/mol
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one + 2 NADPH + 2 H+
2-amino-5-amino-methyl-pyrrolo[2,3-d]pyrimidin-4-one + 2 NADP+
Q46920
natural substrate
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
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late step in biosynthesis of the modified tRNA nucleoside queuosine
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
O31678
late step in biosynthesis of the modified tRNA nucleoside queuosine
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?
7-cyano-7-deazaguanine + 2 NADPH + 2 H+
queuine + 2 NADP+
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late step in biosynthesis of the modified tRNA nucleoside queuosine
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?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
7-formyl-7-deazaguanine
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carbonyl analogue of the imine intermediate, recognized by QueF as weak ligand for binding but not as substrate for reduction or oxidation
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peroxide
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peroxide-induced inactivation of the wild-type enzyme is reversible with thioredoxin
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0061
2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one
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wild-type, pH 7.5, 25°C
0.00025
7-cyano-7-carbaguanine
below 0.25 microM, pH 7.4, 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.024
7-cyano-7-carbaguanine
pH 7.4, 30°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
3
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substrate 5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant E230Q, pH 7.5, 25°C
3.8
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substrate 5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant S90A, pH 7.5, 25°C
4.4
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substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant E230Q, pH 7.5, 25°C
8.7
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substrate 5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant F228W, pH 7.5, 25°C
10.8
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substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant F228W, pH 7.5, 25°C
12.9
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substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant S90A, pH 7.5, 25°C
14.3
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substrate 5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant H229A, pH 7.5, 25°C
17.9
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substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one, mutant H229A, pH 7.5, 25°C
90
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substrate 5-cyanopyrrolo[2,3-d]pyrimidin-4-one, wild-type, pH 7.5, 25°C
117
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substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one, wild-type, pH 7.5, 25°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5 - 8
more than 60% of maximum activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting-drop vapor-diffusion method, space group: P3(1)21. Unit-cell parameters: a = b = 93.52 A, c = 193.76 A
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structure of mutant E97Q, displays an intramolecular disulfide formed between the catalytic Cys55 and a conserved Cys99 located near the active site. This structure exhibits major rearrangement of the loops responsible for substrate binding
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construction of homology model and docking studies of natural and non-natural substrates. Residues C190 and D197 play an essential role in the catalytic mechanism
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homology model based on the crystal structure of nitrile reductase from Vibrio cholerae, PDB ID 3uxv. The side chain of residue Glu89 and the main chain of Ser90 form hydrogen bonds with the ring nitrogen atoms of the substrate. The carboxylate group of Glu230 also forms hydrogen bonds with the substrate preQ0. The aromatic ring of Phe228 may form a pi-pi-stacking interaction with the aromatic ring of preQ0, while the main chain of His229coordinates the keto-functionality of the substrate
hanging drop vapor diffusion method, using 0.04 M sodium dihydrogen phosphate, 0.96 M dipotassium hydrogen phosphate, and 10 mM GTP
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
overproduction in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C99A
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mutant does not compromise enzyme activity. Contrary to wild-type, peroxide-induced inactivation is irreversible
C99S
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mutant does not compromise enzyme activity. Contrary to wild-type, peroxide-induced inactivation is irreversible
C99A
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mutant does not compromise enzyme activity. Contrary to wild-type, peroxide-induced inactivation is irreversible
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C99S
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mutant does not compromise enzyme activity. Contrary to wild-type, peroxide-induced inactivation is irreversible
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C190A
E230Q
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about 4% of wild-type activity for natural substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one
F228W
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about 8% of wild-type activity for natural substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one
H229A
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about 15% of wild-type activity for natural substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one
S90A
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about 10% of wild-type activity for natural substrate 2-amino-5-cyanopyrrolo[2,3-d]pyrimidin-4-one
C190A
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mutation in catalytic residue, no evidence of covalent binding of substrate preQ0. Mutant displays proton uptake
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LINKS TO OTHER DATABASES (specific for EC-Number 1.7.1.13)
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