Information on EC 6.3.4.13 - phosphoribosylamine-glycine ligase

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

EC NUMBER
COMMENTARY hide
6.3.4.13
-
RECOMMENDED NAME
GeneOntology No.
phosphoribosylamine-glycine ligase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
amination
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
5-aminoimidazole ribonucleotide biosynthesis I
-
-
5-aminoimidazole ribonucleotide biosynthesis II
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Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
Metabolic pathways
-
-
purine metabolism
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-
Purine metabolism
-
-
superpathway of 5-aminoimidazole ribonucleotide biosynthesis
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-
SYSTEMATIC NAME
IUBMB Comments
5-phospho-D-ribosylamine:glycine ligase (ADP-forming)
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CAS REGISTRY NUMBER
COMMENTARY hide
9032-01-3
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
gene gart
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Manually annotated by BRENDA team
i.e. Klebsiella pneumoniae
-
-
Manually annotated by BRENDA team
trifunctional enzyme with phosphoribosylamine-glycine ligase activity, glycinamide ribonucleotide transformylase activity, and aminoimidazole ribonucleotide synthetase activity
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-
Manually annotated by BRENDA team
anamorph, Fusarium graminearum. Auxotrophic strains, designated S4B1279 and S4B3008, discovered from a collection of insertional mutants generated by restriction enzyme-mediated integration
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-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum
-
-
-
Manually annotated by BRENDA team
no activity in Mycobacterium leprae
-
-
Manually annotated by BRENDA team
no activity in Mycobacterium leprae
-
-
Manually annotated by BRENDA team
synonym Hansenula polymorpha
UniProt
Manually annotated by BRENDA team
Pigeon
-
-
-
Manually annotated by BRENDA team
OT3
-
-
Manually annotated by BRENDA team
OT3
-
-
Manually annotated by BRENDA team
PCC6803
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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gart and paics mutants have pigmentation defects and microphthalmia
metabolism
physiological function
-
gart and paics function are required for eye growth. IMP feeds into an ATP pathway required for retinoblast proliferation and a GTP pathway required for pigmentation
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + 5-phospho-D-ribosylamine + Gly
ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
show the reaction diagram
ATP + 5-phospho-D-ribosylamine + glycine
ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
show the reaction diagram
-
-
-
?
ATP + 5-phosphoribosylamine + beta-Ala
?
show the reaction diagram
-
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
ATP + 5-phosphoribosylamine + sarcosine
?
show the reaction diagram
-
-
-
-
-
ATP + carbocyclic 5-phosphoribosylamine + Gly
ADP + phosphate + carbocyclic glycinamide ribonucleotide
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
ATP + 5-phospho-D-ribosylamine + glycine
ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
show the reaction diagram
G8EWC8
-
-
-
?
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
-
required
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04588
(+/-)-carbocyclic glycinamide ribonucleotide
-
-
0.07
5'-phosphoribosylamine
-
-
0.00247 - 0.13
5'-phosphoribosylglycinamide
0.056 - 1.01
ATP
3.695
beta-Ala
-
-
0.042 - 0.27
Gly
0.59
glycine
-
pH 7.9, 90C, with Mg2+
0.0064
MgADP-
-
-
0.17
MgATP2-
-
-
0.54
phosphate
-
-
1.2
sarcosine
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.3
5'-phosphoribosylglycinamide
Gallus gallus
-
-
4.8
beta-Ala
Gallus gallus
-
-
7
Gly
Gallus gallus
-
-
3.6
sarcosine
Gallus gallus
-
-
additional information
additional information
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.228
-
-
2.3
selenomethionine-substituted enzyme
4.01
-
pH 7.9, 90C, with Mg+
19
methionine-substituted enzyme
22.8
-
pH 7.9, 90C, with Ca2+
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8
Pigeon
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-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.5
Pigeon
-
7.5-8.0: maximal activity, sharp fall of activity above pH 8.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
Pigeon
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-
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
18
no detectable activity at this temperature
50 - 90
-
enzyme is 8fold more active at 90C than at 50C
50 - 55
Pigeon
-
50C: maximal activity, sharp fall of activity above 55C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
-
Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Aquifex aeolicus (strain VF5)
Aquifex aeolicus (strain VF5)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)
Escherichia coli (strain K12)
Geobacillus kaustophilus (strain HTA426)
Geobacillus kaustophilus (strain HTA426)
Geobacillus kaustophilus (strain HTA426)
Geobacillus kaustophilus (strain HTA426)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45000
gel filtration
48240
calculated from amino acid sequence
49000
gel filtration
50000
gel filtration
55500
-
sucrose density gradient centrifugation
110000
-
trifunctional enzyme with act phosphoribosylamine-glycine ligase activity, glycinamide ribonucleotide transformylase activity, and aminoimidazole ribonucleotide synthetase activity
additional information
-
MW 49000, GAR domain of the trifunctional enzyme, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native enzyme and in complex with ATP, to 2.4 and 1.8 A resolution, respectively. Comparison of crystal structures of GAR-syn from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus. The orientations of the B domains are varied among GAR-syns and the molecular dynamics simulation suggests the mobility of the B domain. The B loop in the B domain fixes the position of the beta- and gamma-phosphate groups of the bound ATP
selenomethionine incorporated enzyme, hanging drop vapor diffusion method
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native enzyme and in complex with phosphate, with AMP and phosphate, and with AMP and glycine, to 2.21, 2.20, 1.9 and 2.21 A resolution, respectively. Comparison of crystal structures of GAR-syn from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus. The orientations of the B domains are varied among GAR-syn's and the molecular dynamics simulation suggests the mobility of the B domain. The B loop in the B domain fixes the position of the beta- and gamma-phosphate groups of the bound ATP
selenomethionine derivative, to 2.8 A resolution. Comparison of crystal structures of GAR-syn from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus. The orientations of the B domains are varied among GAR-syns and the molecular dynamics simulation suggests the mobility of the B domain. The B loop in the B domain fixes the position of the beta- and gamma-phosphate groups of the bound ATP
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80
-
half life 60 h
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
on repeated freeze-thawing activity is lost due to the precipitation of protein
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-18C, stable for at least 1 year
-
-20C, stable for many weeks
-
-80C, slight loss of activity after 3 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
copurification of phosphoribosylamine-glycine ligase and aminoimidazole ribonucleotide synthetase
-
copurification of phosphoribosylamine-glycine ligase and glycinamide ribonucleotide transformylase
-
near homogeneity
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
12-gene cluster encoding nine enzymes for de novo purine nucleotide synthesis
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expressed as the selenomethionine incorporated protein
expressed in Escherichia coli
-
expression in Escherichia coli
overexpressed in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
P294L
loss of function
additional information
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zygotic gart and paic mutants have pigmentation defects in which xanthophore and iridophore pigmentation is almost completely absent, and melanin-derived pigmentation is significantly decreased, even though pigment cells are present in normal amounts and distributions. Zygotic gart and paics mutants are also microphthalmic, resulting from defects in cell cycle exit of proliferative retinoblasts within the developing eye, severe phenotypes, overview
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