Information on EC 6.3.4.13 - phosphoribosylamine-glycine ligase

Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Mark a special word or phrase in this record:
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: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY
6.3.4.13
-
RECOMMENDED NAME
GeneOntology No.
phosphoribosylamine-glycine ligase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
ATP + 5-phospho-D-ribosylamine + glycine = 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
mechanism
Pyrococcus horikoshii OT-3, Synechocystis sp. PCC6803
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
amination
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
5-aminoimidazole ribonucleotide biosynthesis I
-
5-aminoimidazole ribonucleotide biosynthesis II
-
Biosynthesis of secondary metabolites
-
Metabolic pathways
-
Purine metabolism
-
superpathway of 5-aminoimidazole ribonucleotide biosynthesis
-
SYSTEMATIC NAME
IUBMB Comments
5-phospho-D-ribosylamine:glycine ligase (ADP-forming)
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
2-Amino-N-ribosylacetamide 5'-phosphate kinosynthase
-
-
-
-
5'-Phosphoribosylglycinamide synthetase
-
-
-
-
ade5
-
gene encoding a phosphoribosylamine-glycine ligase
EC 6.3.1.3
-
-
formerly
-
GAR synthetase
-
-
-
-
GAR-syn
-
-
GARS
-
-
-
-
GARSase
-
-
-
-
Glycinamide ribonucleotide synthetase
-
-
-
-
Glycineamide ribonucleotide synthetase
-
-
-
-
Phosphoribosylglycinamide synthetase
-
-
-
-
Phosphoribosylglycinamide synthetase
-
-
Phosphoribosylglycineamide synthetase
-
-
-
-
PRG synthetase
-
-
-
-
Synthetase, phosphoribosylglycinamide
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9032-01-3
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
gene gart
-
-
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
-
-
Manually annotated by BRENDA team
trifunctional enzyme with phosphoribosylamine-glycine ligase activity, glycinamide ribonucleotide transformylase activity, and aminoimidazole ribonucleotide synthetase activity
-
-
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
-
-
Manually annotated by BRENDA team
trifunctional enzyme with phosphoribosylamine-glycine ligase activity, glycinamide ribonucleotide transformylase activity, and aminoimidazole ribonucleotide synthetase activity
-
-
Manually annotated by BRENDA team
trifunctional enzyme with phosphoribosylamine-glycine ligase activity, glycinamide ribonucleotide transformylase activity, and aminoimidazole ribonucleotide synthetase activity
-
-
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
Pigeon
-
-
-
Manually annotated by BRENDA team
Pyrococcus horikoshii OT-3
OT3
-
-
Manually annotated by BRENDA team
Synechocystis sp. PCC6803
PCC6803
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
-
gart and paics mutants have pigmentation defects and microphthalmia
metabolism
-
the trifunctional enzyme catalyzes steps 2, 3, and 5 of inosine monophosphate synthesis, followed by paics encoded phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazole succinocarboxamide synthetase, a bifunctional enzyme that catalyzes steps 6 and 7 of this process. Crucial requirement for maternally derived gart and paics. De novo purine synthesis pathway, overview
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 ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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 + Gly
ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
show the reaction diagram
-
-
-
-
-
ATP + 5-phospho-D-ribosylamine + Gly
ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
show the reaction diagram
-
labile product
-
?
ATP + 5-phospho-D-ribosylamine + Gly
ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
show the reaction diagram
Synechocystis sp. PCC6803, Pyrococcus horikoshii OT-3
-
-
-
?
ATP + 5-phosphoribosylamine + beta-Ala
?
show the reaction diagram
-
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
Pigeon
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
r
-
-
ATP + 5-phosphoribosylamine + Gly
ADP + phosphate + 5-phosphoribosylglycinamide
show the reaction diagram
-
r
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
enzyme of purine biosynthetic pathway
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
sequential ordered mechanism of substrate binding and product release in which 5-phosphoribosylamine binds first followed by MgATP2- and then Gly. Phosphate leaves first followed by loss of MgADP- and finally phosphoribosylglycinamide
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
enzyme of the de novo purine biosynthetic pathway
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
enzyme of the de novo purine biosynthetic pathway
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
second step in de novo path of purine biosynthesis
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
second step in de novo path of purine biosynthesis
-
-
-
ATP + 5-phosphoribosylamine + sarcosine
?
show the reaction diagram
-
-
-
-
-
ATP + carbocyclic 5-phosphoribosylamine + Gly
ADP + phosphate + carbocyclic glycinamide ribonucleotide
show the reaction diagram
-
r
-
-
ATP + carbocyclic 5-phosphoribosylamine + Gly
ADP + phosphate + carbocyclic glycinamide ribonucleotide
show the reaction diagram
-
r
-
-
-
additional information
?
-
P15640
second step in de novo purine biosynthesis pathway
-
?
additional information
?
-
-
the enzyme is trifunctional exhibiting phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, and phosphoribosylaminoimidazole synthetase activities, overview
-
-
-
additional information
?
-
Synechocystis sp. PCC6803
-
requirement for ATP and a substrate with a carboxyl group or its relatives, transfer of a phosphate group from ATP to the carboxyl group or its relatives, second step in de novo purine biosynthesis pathway
-
?
additional information
?
-
Pyrococcus horikoshii OT-3
-
requirement for ATP and a substrate with a carboxyl group or its relatives, transfer of a phosphate group from ATP to the carboxyl group or its relatives, second step in de novo purine biosynthesis pathway
-
?
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
-
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
enzyme of purine biosynthetic pathway
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
sequential ordered mechanism of substrate binding and product release in which 5-phosphoribosylamine binds first followed by MgATP2- and then Gly. Phosphate leaves first followed by loss of MgADP- and finally phosphoribosylglycinamide
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
enzyme of the de novo purine biosynthetic pathway
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
enzyme of the de novo purine biosynthetic pathway
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
second step in de novo path of purine biosynthesis
-
-
-
ATP + 5-phosphoribosylamine + Gly
?
show the reaction diagram
-
second step in de novo path of purine biosynthesis
-
-
-
additional information
?
-
P15640
second step in de novo purine biosynthesis pathway
-
?
additional information
?
-
-
the enzyme is trifunctional exhibiting phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, and phosphoribosylaminoimidazole synthetase activities, overview
-
-
-
additional information
?
-
Synechocystis sp. PCC6803, Pyrococcus horikoshii OT-3
-
second step in de novo purine biosynthesis pathway
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Mg2+
-
required
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.04588
-
(+/-)-carbocyclic glycinamide ribonucleotide
-
-
0.07
-
5'-phosphoribosylamine
-
-
0.00247
-
5'-phosphoribosylglycinamide
-
-
0.02
-
5'-phosphoribosylglycinamide
-
-
0.03
-
5'-phosphoribosylglycinamide
-
-
0.13
-
5'-phosphoribosylglycinamide
-
-
0.056
-
ATP
-
at a Mg2+ concentration of 5.7 mM
1.01
-
ATP
-
pH 7.9, 90C, with Mg2+
3.695
-
beta-Ala
-
-
0.042
-
Gly
-
-
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]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2.3
-
5'-phosphoribosylglycinamide
-
-
4.8
-
beta-Ala
-
-
3.6
-
Sarcosine
-
-
additional information
-
additional information
-
-
-
additional information
-
additional information
-
-
-
additional information
-
additional information
-
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.228
-
-
-
2.3
-
P15640
selenomethionine-substituted enzyme
4.01
-
-
pH 7.9, 90C, with Mg+
7.2
-
-
-
19
-
P15640
methionine-substituted enzyme
22.8
-
-
pH 7.9, 90C, with Ca2+
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
8
Pigeon
-
-
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
8.5
Pigeon
-
7.5-8.0: maximal activity, sharp fall of activity above pH 8.5
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
50
-
Pigeon
-
-
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
18
-
P15640
no detectable activity at this temperature
50
55
Pigeon
-
50C: maximal activity, sharp fall of activity above 55C
50
90
-
enzyme is 8fold more active at 90C than at 50C
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
Pigeon
-
-
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
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
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
45000
-
Q5SK40, -
gel filtration
48240
-
P15640
calculated from amino acid sequence
49000
-
P15640
gel filtration
50000
-
-, Q5L3C7
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 ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 45253, calculation from nucleotide sequence
?
-
x * 112000, enzyme protein with glycinamide phosphoribosylamine-glycine ligase and aminoimidazole ribonucleotide synthetase activity, SDS-PAGE
?
-
GAR domain of the multifunctional enzyme has a MW of 49000, SDS-PAGE, the multifunctional enzyme has a MW of 110000, SDS-PAGE
?
-
x * 47000
?
-
x * 45945, calculation from nucleotide sequence
monomer
-, Q5L3C7
1 * 50000, SDS-PAGE
monomer
Q5SK40, -
1 * 45000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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
-, O66949
selenomethionine incorporated enzyme, hanging drop vapor diffusion method
-
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
-, Q5L3C7
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
Q5SK40, -
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
80
-
-
half life 60 h
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
on repeated freeze-thawing activity is lost due to the precipitation of protein
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
LITERATURE
near homogeneity
-
copurification of phosphoribosylamine-glycine ligase and glycinamide ribonucleotide transformylase
-
copurification of phosphoribosylamine-glycine ligase and aminoimidazole ribonucleotide synthetase
-
-
Pigeon
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli
-
expression in Escherichia coli
-, O66949
12-gene cluster encoding nine enzymes for de novo purine nucleotide synthesis
-
expressed as the selenomethionine incorporated protein
P15640
expression in Escherichia coli
-, Q5L3C7
overexpressed in Escherichia coli
-
expression in Escherichia coli
Q5SK40, -
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
P294L
P15640
loss of function
additional information
-
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