Information on EC 5.3.1.3 - D-arabinose isomerase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY hide
5.3.1.3
-
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
-
-
D-arabinose degradation II
-
-
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
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain 14A
-
-
Manually annotated by BRENDA team
strain B/r
-
-
Manually annotated by BRENDA team
40bXX
-
-
Manually annotated by BRENDA team
strain M-7
-
-
Manually annotated by BRENDA team
strain PRL-R3
-
-
Manually annotated by BRENDA team
strain W70, 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
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
stimulates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-amino-2-methyl-1,3-propanediol
-
-
dithioerythritol
-
-
dithiothreitol
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competitive
Dulcitol
-
-
EDTA
-
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
-
-
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
0.0287
D-Altrose
Caldicellulosiruptor saccharolyticus
A4XJ56
-
0.1823
D-arabinose
Caldicellulosiruptor saccharolyticus
A4XJ56
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.73
-
after purification, L-galactose as substrate
1
-
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
-
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
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60000
-
SDS-PAGE
67000
-
SDS-PAGE
68000
determined by SDS-PAGE
204000
homotrimer, determined by gel filtration
250000
-
gel filtration
342000
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strain B/r, high-speed equilibrium sedimentation
355000
-
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
-
-
674955
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55
-
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
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
2°C, crystalline enzyme is stable as a sediment in polyethylene glycol solution for at least 1 month
-
stable for more than 1 month in 50 mM Tris-HCl buffer at pH 7.5 containing 1 mM MnCl2 and mercaptoethanol
-
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
-
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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