Information on EC 5.3.1.13 - arabinose-5-phosphate isomerase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.3.1.13
-
RECOMMENDED NAME
GeneOntology No.
arabinose-5-phosphate isomerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-Arabinose 5-phosphate = D-ribulose 5-phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
intramolecular oxidoreduction
-
-
-
-
isomerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
CMP-3-deoxy-D-manno-octulosonate biosynthesis
-
-
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis
-
-
Lipopolysaccharide biosynthesis
-
-
Metabolic pathways
-
-
CMP-KDO biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
D-arabinose-5-phosphate aldose-ketose-isomerase
The enzyme is involved in the pathway for synthesis of 3-deoxy-D-manno-octulosonate (Kdo), a component of bacterial lipopolysaccharides and plant call walls.
CAS REGISTRY NUMBER
COMMENTARY hide
9023-86-3
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
wild type and CDY176 deletion mutant
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3-deoxy-D-arabinose 5-phosphate
3-deoxy-D-glycero-pentulose 5-phosphate
show the reaction diagram
-
KdsD converts 3-deoxy-A5P to 3-deoxy-Ru5P, but the catalysis proceeds tenfold slower than for the natural substrate isomerization
-
-
?
3-deoxy-D-threo-pentofuranose 5-phosphate
3-deoxy-D-glycero-pentulose 5-phosphate
show the reaction diagram
4-deoxy-D-arabinose 5-phosphate
4-deoxy-D-glycero-pentulose 5-phosphate
show the reaction diagram
-
KdsD converts 4-deoxy-A5P to 4-deoxy-Ru5P, but the catalysis proceeds slower than for the natural substrate isomerization
-
-
?
4-deoxy-D-threo-arabinose 5-phosphate
4-deoxy-D-glycero-pentulose 5-phosphate
show the reaction diagram
the isomerization rate for this compound is 2fold higher than that of the natural substrate
-
-
?
4-deoxy-D-threo-pentofuranose 5-phosphate
4-deoxy-D-glycero-pentulose 5-phosphate
show the reaction diagram
-
the catalytic efficiency is comparable with the natural substrate D-arabinose 5-phosphate
-
-
?
D-Arabinose 5-phosphate
D-Ribulose 5-phosphate
show the reaction diagram
D-Ribulose 5-phosphate
?
show the reaction diagram
D-ribulose 5-phosphate
D-arabinose 5-phosphate
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
D-Arabinose 5-phosphate
D-Ribulose 5-phosphate
show the reaction diagram
D-Ribulose 5-phosphate
?
show the reaction diagram
D-ribulose 5-phosphate
D-arabinose 5-phosphate
show the reaction diagram
-
first enzyme in the biosynthesis of 3-deoxy-D-manno-octulosonate
-
r
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ba2+
-
stimulates activity
Co2+
-
stimulates activity
Cu2+
-
stimulates activity
Ni2+
-
stimulates activity
additional information
Ba2+, Co2+, Ni2+ have no effect
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2R,3R)-2,3-dihydroxy-4-(hydroxyamino)-4-oxobutyl phosphate
-
-
(2R,3R)-4-amino-2,3-dihydroxy-4-oxobutyl phosphate
-
-
(2S,3R)-2,3-bis(acetyloxy)-4-(hydroxyamino)-4-oxobutyl phosphate
-
-
Erythronic acid 4-phosphate
-
best inhibitor
Heavy metal ions
-
-
-
oxido(dioxo)[(2R,3R)-N,2,3-trihydroxy-4-(hydroxy-kO)butanamidato]phosphate(2-)
-
-
p-hydroxymercuribenzoate
Phosphorylated sugars
-
in a series of nonphosphorylated sugars, the order of decreasing inhibitory activity is as follows: aldonic acids, alditols, aldoses
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[(2R,3R)-1-(hydroxy-kO)-4-(hydroxyamino)-4-oxobutane-2,3-diyl diacetatato](oxido)dioxophosphate(2-)
-
-
[(2R,3R)-2,3-dihydroxy-4-(hydroxy-kO)butanamidato](oxido)dioxophosphate(2-)
-
-
[(4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl phosphate
-
-
[(4R,5R)-N-hydroxy-5-[(hydroxy-kO)methyl]-2,2-dimethyl-1,3-dioxolane-4-carboxamidato](oxido)dioxophosphate(2-)
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 1.98
D-arabinose 5-phosphate
0.3 - 0.7
D-ribulose 5-phosphate
0.09 - 0.15
ribulose 5-phosphate
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
15 - 218
D-arabinose 5-phosphate
10.5 - 255
D-ribulose 5-phosphate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8.8
D-arabinose 5-phosphate
Escherichia coli
-
pH 6.6, 37C
538
15
D-ribulose 5-phosphate
Escherichia coli
-
pH 6.6, 37C
443
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.035
oxido(dioxo)[(2R,3R)-N,2,3-trihydroxy-4-(hydroxy-kO)butanamidato]phosphate(2-)
-
at 37C, pH not specified in the publication
0.007
[(2R,3R)-1-(hydroxy-kO)-4-(hydroxyamino)-4-oxobutane-2,3-diyl diacetatato](oxido)dioxophosphate(2-)
-
at 37C, pH not specified in the publication
0.01
[(2R,3R)-2,3-dihydroxy-4-(hydroxy-kO)butanamidato](oxido)dioxophosphate(2-)
-
at 37C, pH not specified in the publication
3
[(4R,5R)-N-hydroxy-5-[(hydroxy-kO)methyl]-2,2-dimethyl-1,3-dioxolane-4-carboxamidato](oxido)dioxophosphate(2-)
-
at 37C, pH not specified in the publication
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.035
(2R,3R)-2,3-dihydroxy-4-(hydroxyamino)-4-oxobutyl phosphate
Francisella tularensis
-
pH and temperature not specified in the publication
0.01
(2R,3R)-4-amino-2,3-dihydroxy-4-oxobutyl phosphate
Francisella tularensis
-
pH and temperature not specified in the publication
0.007
(2S,3R)-2,3-bis(acetyloxy)-4-(hydroxyamino)-4-oxobutyl phosphate
Francisella tularensis
-
pH and temperature not specified in the publication
0.001 - 0.003
Zn2+
Escherichia coli
-
0.01 mM, complete inhibition, IC50: 0.001-0.003 mM
3
[(4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl phosphate
Francisella tularensis
-
pH and temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.092
-
mutant enzyme K56A, in TrisHCl, (pH 8.5, 50 mM), at 37C
29.5
-
recombinant wild type enzyme, in TrisHCl, (pH 8.5, 50 mM), at 37C
29.55
-
pH and temperature not specified in the publication
additional information
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 7.5
-
only trace A5P isomerase activity observed below pH 5.5 or above pH 7.5
7 - 10
-
pH 7.0: about 70% of maximal activity, pH 10.0: about 70% of maximal activity
7.5 - 8.5
-
about 90% of maximal activity at pH 7.5 and 8.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
assay at
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20888
-
x * 20888, mass spectrometry
21000
-
x * 21000, SDS-PAGE
33909
-
4 * 33909, electrospray ionization mass spectrometry
34000
-
x * 34000, SDS-PAGE
34067
-
x * 34067, calculated from amino acid sequence
73000
-
gel filtration
122000
133000
135000
-
gel filtration
145000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 34000, SDS-PAGE; x * 34067, calculated from amino acid sequence
tetramer
trimer or tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
mutant enzyme K59A, sitting drop vapor diffusion method, using 20% PEG 8K and 0.1 M HEPES, pH 7.5
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80C, stable for at least 1 month
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
; metal-affinity column chromatography
-
ammonium sulfate precipitation and MonoQ column chromatography
-
Ni-chelate affinity column chromatography
-
Ni-NTA agarose column chromatography
-
Ni-NTA agarose column chromatography, gel filtration
-
of the recombinant protein by Q-Sepharose fast flow column chromatography
recombinant
-
recombinant GutQ
-
recombinant His-tagged KdsD from Escherichia coli strain Bl21(DE3) by nickel affinity chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
-
expressed in Escherichia coli BB-8 cells
-
expressed in Escherichia coli BL21(DE3) cells
-
expressed in Escherichia coli; expressed in Escherichia coli BL21(DE3) cells
-
expression in Escherichia coli
-
GutQ. GutQ is a second copy of D-arabinose 5-phosphate isomerase (API) from the genome of Escherichia coli K-12, with biochemical properties similar to those of KdsD
-
kdsD and gutQ, API is encoded by the two paralogous genes, which may substitute for each other, expression of His-tagged KdsD in Escherichia coli strain BL21(DE3), subcloning in strain DH5alpha
-
overexpression in Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H88A
-
the enzyme site-specific mutant is able to catalyze the isomerization of A5P to R5P in vitro with 9.5% of the wild type protein activity
K59A
-
catalytically inactive
H190A
-
inactive
H85A
-
inactive
K56A
-
the mutant shows 0.31% residual activity compared to the wild type enzyme
additional information
-
the deletion mutants CDY17615 are transformed with 15 low copy number constructs to study the abilty to biofilms
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