Information on EC 3.5.4.25 - GTP cyclohydrolase II

Word Map on EC 3.5.4.25
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
3.5.4.25
-
RECOMMENDED NAME
GeneOntology No.
GTP cyclohydrolase II
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of C-N bonds
hydrolysis of phosphoesters
-
-
-
-
hydrolysis of phosphoric ester
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)
-
-
Biosynthesis of secondary metabolites
-
-
flavin biosynthesis I (bacteria and plants)
-
-
flavin biosynthesis III (fungi)
-
-
Metabolic pathways
-
-
Riboflavin metabolism
-
-
flavin biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
GTP 7,8-8,9-dihydrolase (diphosphate-forming)
Two C-N bonds are hydrolysed, releasing formate, with simultaneous removal of the terminal diphosphate.
CAS REGISTRY NUMBER
COMMENTARY hide
56214-35-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
guanosine triphosphate cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase; gene NbRibA encoding the bifunctional guanosine triphosphate cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
NbRibA-silenced plants show slightly dwarf phenotypes, levels of endogenous riboflavin and its derivatives FMN and FAD are decreased in NbRibA-silenced Nicotiana benthamiana plants. Silencing of NbRibA compromises not only hypersensitive response cell death, but also the NO and reactive oxygen species production induced by INF1 elicitin and a constitutively active form of NbMEK2, and also induces high susceptibility to oomycete Phytophthora infestans and ascomycete Colletotrichum orbiculare. Compromised radical production and hypersensitive response cell death induced by INF1 in NbRibA-silenced leaves are rescued by adding riboflavin, FMN or FAD
metabolism
physiological function
-
3,4-dihydroxy 2-butanone 4-phosphate synthase, DHBPS EC 4.1.99.12, and GTP cyclohydrolase-II, GTPCH-II, are the two initial enzymes involved in riboflavin biosynthesis pathway, which is essential for the pathogen
additional information
-
bifunctional enzyme with 3,4-dihydroxy 2-butanone 4-phosphate synthase, DHBPS EC 4.1.99.12, and GTP cyclohydrolase-II, GTPCH-II, domains at N- and C-termini, respectively
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate + H2O
?
show the reaction diagram
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone triphosphate + H2O
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate
show the reaction diagram
-
formamide-type intermediate analogue
-
-
?
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone triphosphate + H2O
formate + 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate
show the reaction diagram
dGTP + H2O
formate + 2,5-diamino-6-hydroxy-4-(5-phospho-deoxyribosylamino)pyrimidine + diphosphate
show the reaction diagram
-
-
-
-
?
GTP + 3 H2O
formate + 2,5-diamino-6-beta-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate
show the reaction diagram
GTP + H2O
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate + ?
show the reaction diagram
enzyme catalyzes the first step in the biosynthesis of riboflavin
-
-
?
GTP + H2O
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate + ?
show the reaction diagram
GTP + H2O
formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate
show the reaction diagram
GTP + H2O
formate + 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + diphosphate
show the reaction diagram
GTP + H2O
formate + 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + diphosphate
show the reaction diagram
GTP + H2O
formate + 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
GTP + 3 H2O
formate + 2,5-diamino-6-beta-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate
show the reaction diagram
-
first committed step in the biosynthesis of riboflavin, overview
-
-
?
GTP + H2O
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate + ?
show the reaction diagram
O88011, Q9EWJ8, Q9KYI5
enzyme catalyzes the first step in the biosynthesis of riboflavin
-
-
?
GTP + H2O
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate + ?
show the reaction diagram
O88011, Q9EWJ8, Q9KYI5
-
-
-
?
GTP + H2O
formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate
show the reaction diagram
GTP + H2O
formate + 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + diphosphate
show the reaction diagram
GTP + H2O
formate + 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + diphosphate
show the reaction diagram
GTP + H2O
formate + 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate + diphosphate
show the reaction diagram
-
first committed step in the biosynthesis of riboflavin, overview
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
diphosphate
phosphate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.031 - 0.122
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate
0.3
8-oxo-dGTP
-
-
0.21
8-oxo-GTP
-
-
0.008 - 0.41
GTP
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05 - 0.1
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate
0.0033 - 432
GTP
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.4 - 2.1
GTP
37
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.024
diphosphate
-
pH 8.5, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.002
-
purified recombinant mutant C65S, substrate GTP cleaved to GMP
0.003
-
purified recombinant mutant C67S, substrate GTP cleaved to GMP
0.01
-
purified recombinant mutant C54S, substrate GTP cleaved to GMP
0.015
-
purified recombinant wild-type enzyme, substrate 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone triphosphate cleaved to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate
0.016
-
purified recombinant wild-type enzyme, substrate GTP cleaved to GMP
0.025
-
purified recombinant wild-type enzyme, substrate dGTP cleaved to dGMP
0.038
-
purified recombinant wild-type enzyme, substrate dGTP cleaved to 2,5-diamino-6-hydroxy-4-(5-phospho-deoxyribosylamino)pyrimidine
0.08
-
recombinant enzyme
0.122
-
purified recombinant wild-type enzyme, substrate 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone triphosphate cleaved to 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
0.182
-
purified recombinant wild-type enzyme, substrate GTP cleaved to 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
53
-
fusion protein without a signal sequence
165
-
fusion protein with a signal sequence
additional information
-
activity of the mutant enzyme C54S, C65S, and C67S with the different substrates, overview, best substrate is GTP being cleaved to GMP
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
-
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2 - 10.5
-
half of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8
calculated from amino acid sequence
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Helicobacter pylori (strain ATCC 700392 / 26695)
Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22000
-
alpha2, 2 * 22000, SDS-PAgGE
34800
calculated from amino acid sequence
46100
monomer, determined by SDS-PAGE
48163
2 * 48163, MALDI-TOF mass spectrometry
170000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
alpha2, 2 * 22000, SDS-PAgGE
homodimer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
selenomethionine-labeled crystals, 1.54 A resolution
-
sitting drop vapor diffusion method, using 0.1 M Na HEPES pH 7.5, 15% (w/v) PEG 8000
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60
-
enzyme loses rapidly activity about 60C
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 1 mg/ml, pH8, in presence of EDTA and an excess of Mg2+, quite stable
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, Ni-NTA column chromatography, and Sephacryl S-200 gel filtration
DEAE-Sephadex column chromatography, Q-Sepharose column chromatography, butyl-Sepharose column chromatography, and Sephacryl S-300 gel filtration
-
purification of wild type enzyme and its mutants by nickel affinity chromatography, site-directed variants are expressed in the native state and purified to homogeneity by ion exchange and hydrophobic interaction chromatographic steps; purification of wild type enzyme and its mutants by nickel affinity chromatography, site-directed variants are expressed in the native state and purified to homogeneity by ion exchange and hydrophobic interaction chromatographic steps; purification of wild type enzyme and its mutants by nickel affinity chromatography, site-directed variants are expressed in the native state and purified to homogeneity by ion exchange and hydrophobic interaction chromatographic steps
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expression in Escherichia coli
expression of wild-type and mutant enzymes
-
gene ribA2, DNA and amino acid sequence analysis and comparison of DHBPS/GTPCH-II sequences
-
overexpression and purification of wild type and site-directed variants of GCH II; overexpression and purification of wild type and site-directed variants of GCH II; overexpression and purification of wild type and site-directed variants of GCH II
overexpression in strain 1012 by gene insertion in the sacB locus
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Y210C/A290T/Q293R/A296T/K322R/F339Y/M361I
-
the mutant shows a 2fold increase in GTP cyclohydrolase II activity and a 4fold increase in the Km value with GTP as the substrate. Using 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate as the substrate, the mutant shows a rate enhancement by a factor of about 2 and an increase in the Km value by a factor of about 5
Y210C/A290T/Q293R/A296T/K322R/M361I
-
the mutant shows increased kcat and Km values compared to the wild type enzyme using GTP and 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate as the substrate
C54S
-
site-directed mutagenesis, mutation results in proteins devoid of bound zinc and unable to release formate from the imidazole ring of GTP or from the intermediate analogue 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate, however, the mutant enzyme is still capable to release diphosphate from GTP and from the formamide-type intermediate analogue
C65S
-
site-directed mutagenesis, mutation results in proteins devoid of bound zinc and unable to release formate from the imidazole ring of GTP or from the intermediate analogue 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate, however, the mutant enzyme is still capable to release diphosphate from GTP and from the formamide-type intermediate analogue
C67S
-
site-directed mutagenesis, mutation results in proteins devoid of bound zinc and unable to release formate from the imidazole ring of GTP or from the intermediate analogue 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate, however, the mutant enzyme is still capable to release diphosphate from GTP and from the formamide-type intermediate analogue
C396S
site-directed mutagenesis,
E154D
site-directed mutagenesis,
D127A
about 10fold less efficient than the wild-type protein
G209D
about 10fold less efficient than the wild-type protein
M120A
generated by site-directed mutagenesis
M120C
generated by site-directed mutagenesis
M120D
generated by site-directed mutagenesis
M120E
generated by site-directed mutagenesis
M120F
generated by site-directed mutagenesis
M120G
generated by site-directed mutagenesis
M120H
generated by site-directed mutagenesis
M120I
generated by site-directed mutagenesis
M120K
generated by site-directed mutagenesis
M120N
generated by site-directed mutagenesis
M120Q
generated by site-directed mutagenesis
M120S
generated by site-directed mutagenesis
M120T
generated by site-directed mutagenesis
M120W
generated by site-directed mutagenesis
M120Y
generated by site-directed mutagenesis
R83H
mutant substantially impaired in overall activity
Y123M
about 10fold less efficient than the wild-type protein, produces exclusively 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate
Y326F
generated by site-directed mutagenesis, catalytically inactive variant
Y326M
generated by site-directed mutagenesis, catalytically inactive variant
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pharmacology
-
enzyme is a potential drug target, since numerous pathogenic microorganims are absolutely dependent on endogenous synthesis of riboflavin, target for development of bactericidal inhibitors
synthesis
-
the enzyme is essential for industrial riboflavin production by Bacillus subtilis overproducing strains, overview
Show AA Sequence (10471 entries)
Longer loading times are possible. Please use the Sequence Search for a specific query.