Information on EC 5.3.1.3 - D-arabinose isomerase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.3.1.3
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RECOMMENDED NAME
GeneOntology No.
D-arabinose isomerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-Arabinose = D-ribulose
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
D-arabinose degradation I
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D-arabinose degradation II
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degradation of pentoses
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SYSTEMATIC NAME
IUBMB Comments
D-arabinose aldose-ketose-isomerase
Requires a divalent metal ion (the enzyme from the bacterium Escherichia coli prefers Mn2+). The enzyme binds the closed form of the sugar and catalyses ring opening to generate a form of open-chain conformation that facilitates the isomerization reaction, which proceeds via an ene-diol mechanism [3]. The enzyme catalyses the aldose-ketose isomerization of several sugars. Most enzymes also catalyse the reaction of EC 5.3.1.25, L-fucose isomerase [3]. The enzyme from the bacterium Falsibacillus pallidus also converts D-altrose to D-psicose [4]. cf. EC 5.3.1.4, L-arabinose isomerase.
CAS REGISTRY NUMBER
COMMENTARY hide
9023-81-8
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
wild type enzyme and constitutive mutants
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-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-altrose
D-psicose
show the reaction diagram
D-Arabinose
?
show the reaction diagram
D-Arabinose
D-Ribulose
show the reaction diagram
D-galactose
D-tagatose
show the reaction diagram
-
-
-
-
r
D-Lyxose
D-Xylulose
show the reaction diagram
D-Mannose
D-Fructose
show the reaction diagram
D-Xylose
D-Xylulose
show the reaction diagram
-
-
-
-
r
L-Fucose
?
show the reaction diagram
L-Fucose
L-Fuculose
show the reaction diagram
L-galactose
L-tagatose
show the reaction diagram
L-glucose
L-fructose
show the reaction diagram
-
-
-
-
r
L-Lyxose
L-Xylulose
show the reaction diagram
L-ribose
L-ribulose
show the reaction diagram
-
-
-
-
r
L-Xylose
L-Xylulose
show the reaction diagram
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-altrose
D-psicose
show the reaction diagram
D-Arabinose
?
show the reaction diagram
D-Arabinose
D-Ribulose
show the reaction diagram
L-Fucose
?
show the reaction diagram
L-galactose
L-tagatose
show the reaction diagram
A4XJ56
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-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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stimulates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-amino-2-methyl-1,3-propanediol
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dithioerythritol
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dithiothreitol
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competitive
Dulcitol
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EDTA
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plus L-His
His
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L-His: activates in presence of Mn2+, strong noncompetitive inhibition without metal ion or in presence of Mg2+, Sr2+, Ca2+, Na+ or K+. D-His has almost the same effect as L-His
L-arabitol
ribitol
sorbitol
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tert-Butylamine
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weak
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
98 - 280
D-arabinose
35 - 55
L-fucose
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.73
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after purification, L-galactose as substrate
1
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after purification, D-altrose as substrate; after purification, D-xylose as substrate; after purification, L-ribose as substrate
1.3
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after purification, D-galactose as substrate; after purification, D-lyxose as substrate
1.9
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after purification, L-glucose as substrate
2.7
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after purification, L-lyxose as substrate
2.8
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after purification, D-mannose as substrate
3 - 8
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after purification, L-fucose as substrate
4.7
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after purification, L-xylose as substrate
25.1
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D-arabinose, constitutive mutant 502
36.5
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after purification, D-arabinose as substrate
43.5
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L-fucose, constitutuve mutant 502
63.3
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Escherichia coli K-12
63.7
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Escherichia coli B/r
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 10
9.3
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D-arabinose; L-fucose
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 10
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7.0: sharp decrease in activity below, 8.0-10.0: maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60000
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SDS-PAGE
64976
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6 * 64976, crystallographic data
67000
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SDS-PAGE
68000
determined by SDS-PAGE
84600
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4 * 84600, Escherichia coli B/r, high speed sedimentation of enzyme dissociated into subunits by protonation at pH 2 or dialysis against buffer containing 8 M urea
90900
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4 * 90900, Escherichia coli K-12, high speed sedimentation of enzyme dissociated into subunits by protonation at pH 2 or dialysis against buffer containing 8 M urea
204000
homotrimer, determined by gel filtration
250000
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gel filtration
342000
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strain B/r, high-speed equilibrium sedimentation
355000
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strain K-12, high-speed equilibrium sedimentation
390000
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting drop vapour diffusion method, with 100 mM citrate buffer (final pH 6.0) and 20% (w/v) PEG 3000
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three X-ray structures of D-arabinose isomerase in complexes with 2-methyl-2,4-pentadiol, glycerol and L-fucitol are determined at resolutions of 1.77, 1.60 and 2.60 A, respectively
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9
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674955
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55
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about 40% loss of activity after 10 min without dithiothreitol, stable in presence of dithiothreitol
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
dithiothreitol protects from thermal inactivation at 55 C
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
2°C, crystalline enzyme is stable as a sediment in polyethylene glycol solution for at least 1 month
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stable for more than 1 month in 50 mM Tris-HCl buffer at pH 7.5 containing 1 mM MnCl2 and mercaptoethanol
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
of the wild type protein by Q-sepharose HP and Phenyl-sepharose column chromatography
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Q Sepharose column chromatography, Resource PHE column chromatography, and Resource Q column chromatography
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using an anion-exchange column, Q Sepharose high performance, a hydrophobic interaction column, RESOURCE PHE, and an anion-exchange column, RESOURCE Q
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli strain JM109
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for over-expression in Escherichia coli JM109 cells
into the vector pGEM-T Easy, and subsequently into the vector pET15b for expression in Escherichia coli ER2566 cells
nucleotide sequence of the gene fucI
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organization of the fuc regulon specifying L-fucose dissimilation as determined by gene cloning
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overexpression in Escherichia coli
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