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
5.3.1.3
-
RECOMMENDED NAME
GeneOntology No.
D-arabinose isomerase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
D-Arabinose = D-ribulose
show the reaction diagram
-
-
-
-
D-Arabinose = D-ribulose
show the reaction diagram
protein environment suggests strongly that the reaction belongs to the ene-diol type
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
isomerization
-
-
-
-
isomerization
-
-
isomerization
C0SSE7
-
isomerization
Klebsiella pneumoniae 40bXX
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
D-arabinose degradation I
-
D-arabinose degradation II
-
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.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D-AI
Aeribacillus pallidus 14A
-
-
-
D-arabinose aldose-ketose-isomerase
-
-
D-arabinose aldose-ketose-isomerase
Klebsiella pneumoniae 40bXX
-
-
-
D-Arabinose isomerase
-
-
-
-
D-Arabinose isomerase
-
-
D-Arabinose isomerase
C0SSE7
L-fucose isomerase, bifunctional enzyme
D-Arabinose isomerase
Aeribacillus pallidus 14A
-
-
-
D-Arabinose isomerase
A4XJ56
L-fucose isomerase, bifunctional enzyme
D-Arabinose isomerase
-
D-AI
D-Arabinose isomerase
Klebsiella pneumoniae 40bXX
-
D-AI
-
D-arabinose ketol-isomerase
-
-
-
-
D-Arabinose(L-fucose) isomerase
-
-
-
-
EC 5.1.3.25
-
-
related
-
Isomerase, arabinose
-
-
-
-
L-Fucose isomerase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9023-81-8
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
strain 14A
-
-
Manually annotated by BRENDA team
Aeribacillus pallidus 14A
strain 14A
-
-
Manually annotated by BRENDA team
strain B/r; strain K-12
-
-
Manually annotated by BRENDA team
strain K-12; wild type and mutant strains which constitutively synthesize the enzyme
-
-
Manually annotated by BRENDA team
Escherichia coli B/r
strain B/r
-
-
Manually annotated by BRENDA team
mutants which are capable of utilizing D-arabinose as a sole source of carbon and energy for growth
-
-
Manually annotated by BRENDA team
strain PRL-R3
-
-
Manually annotated by BRENDA team
strain W70, wild type enzyme and constitutive mutants
-
-
Manually annotated by BRENDA team
wild type strain PRL-R3 and two constitutive mutants, 502 and 510
-
-
Manually annotated by BRENDA team
Klebsiella pneumoniae 40bXX
40bXX
-
-
Manually annotated by BRENDA team
Klebsiella pneumoniae M-7
strain M-7
-
-
Manually annotated by BRENDA team
Klebsiella pneumoniae PRL-R3
strain PRL-R3
-
-
Manually annotated by BRENDA team
Klebsiella pneumoniae W70
strain W70, wild type enzyme and constitutive mutants
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-altrose
D-psicose
show the reaction diagram
-
-
-
-
r
D-altrose
D-psicose
show the reaction diagram
-
-
-
-
?
D-altrose
D-psicose
show the reaction diagram
A4XJ56
-
-
-
?
D-altrose
D-psicose
show the reaction diagram
C0SSE7
-
-
-
?
D-altrose
D-psicose
show the reaction diagram
Aeribacillus pallidus 14A
-
-
-
-
?
D-Arabinose
D-Ribulose
show the reaction diagram
-
-
-
-
-
D-Arabinose
D-Ribulose
show the reaction diagram
-
-
-
-
D-Arabinose
D-Ribulose
show the reaction diagram
-
-
-
-
-
D-Arabinose
D-Ribulose
show the reaction diagram
-
-
-
-
r
D-Arabinose
D-Ribulose
show the reaction diagram
-
-
-
-
?
D-Arabinose
D-Ribulose
show the reaction diagram
A4XJ56
-
-
-
?
D-Arabinose
D-Ribulose
show the reaction diagram
C0SSE7
-
-
-
?
D-Arabinose
D-Ribulose
show the reaction diagram
Escherichia coli B/r
-
-
-
-
-
D-Arabinose
D-Ribulose
show the reaction diagram
Klebsiella pneumoniae PRL-R3
-
-
-
-
D-Arabinose
D-Ribulose
show the reaction diagram
Aeribacillus pallidus 14A
-
-
-
-
?
D-Arabinose
D-Ribulose
show the reaction diagram
Klebsiella pneumoniae 40bXX
-
-
-
-
r
D-Arabinose
?
show the reaction diagram
-
L-fuculose 1-phosphate is the inducer
-
-
-
D-Arabinose
?
show the reaction diagram
-
the enzyme catalyzes the first reaction in the degradation of D-arabinose
-
-
-
D-Arabinose
?
show the reaction diagram
-
deficiency of the enzyme results in loss of activity to utilize D-arabinose
-
-
-
D-galactose
D-tagatose
show the reaction diagram
-
-
-
-
r
D-Lyxose
D-Xylulose
show the reaction diagram
Klebsiella pneumoniae, Klebsiella pneumoniae 40bXX
-
-
-
-
r
D-Mannose
D-Fructose
show the reaction diagram
Klebsiella pneumoniae, Klebsiella pneumoniae 40bXX
-
-
-
-
r
D-Xylose
D-Xylulose
show the reaction diagram
-
-
-
-
r
L-Fucose
L-Fuculose
show the reaction diagram
-
-
-
-
-
L-Fucose
L-Fuculose
show the reaction diagram
-
-
-
-
L-Fucose
L-Fuculose
show the reaction diagram
-
-
-
-
-
L-Fucose
L-Fuculose
show the reaction diagram
-
-
-
-
r
L-Fucose
L-Fuculose
show the reaction diagram
-
-
-
-
?
L-Fucose
L-Fuculose
show the reaction diagram
Klebsiella pneumoniae M-7
-
-
-
-
-
L-Fucose
L-Fuculose
show the reaction diagram
Escherichia coli B/r
-
-
-
-
-
L-Fucose
L-Fuculose
show the reaction diagram
Aeribacillus pallidus 14A
-
-
-
-
?
L-Fucose
L-Fuculose
show the reaction diagram
Escherichia coli K12
-
-
-
-
-
L-Fucose
L-Fuculose
show the reaction diagram
Klebsiella pneumoniae W70
-
-
-
-
-
L-Fucose
?
show the reaction diagram
-
enzyme of the metabolic pathway of L-fucose
-
-
-
L-Fucose
?
show the reaction diagram
-
L-fucose catabolic enzyme
-
-
-
L-Fucose
?
show the reaction diagram
Escherichia coli K12
-
enzyme of the metabolic pathway of L-fucose
-
-
-
L-Fucose
?
show the reaction diagram
Klebsiella pneumoniae W70
-
L-fucose catabolic enzyme
-
-
-
L-galactose
L-tagatose
show the reaction diagram
-
-
-
-
r
L-galactose
L-tagatose
show the reaction diagram
-
-
-
-
?
L-galactose
L-tagatose
show the reaction diagram
A4XJ56
-
-
-
?
L-galactose
L-tagatose
show the reaction diagram
Aeribacillus pallidus 14A
-
-
-
-
?
L-glucose
L-fructose
show the reaction diagram
-
-
-
-
r
L-Lyxose
L-Xylulose
show the reaction diagram
Klebsiella pneumoniae, Klebsiella pneumoniae 40bXX
-
-
-
-
r
L-ribose
L-ribulose
show the reaction diagram
-
-
-
-
r
L-Xylose
L-Xylulose
show the reaction diagram
-
-
-
-
L-Xylose
L-Xylulose
show the reaction diagram
-
-
-
-
r
L-Xylose
L-Xylulose
show the reaction diagram
-
-
-
-
?
L-Xylose
L-Xylulose
show the reaction diagram
Klebsiella pneumoniae PRL-R3
-
-
-
-
L-Xylose
L-Xylulose
show the reaction diagram
Aeribacillus pallidus 14A
-
-
-
-
?
L-Xylose
L-Xylulose
show the reaction diagram
Klebsiella pneumoniae 40bXX
-
-
-
-
r
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
D-altrose
D-psicose
show the reaction diagram
A4XJ56
-
-
-
?
D-altrose
D-psicose
show the reaction diagram
C0SSE7
-
-
-
?
D-Arabinose
D-Ribulose
show the reaction diagram
A4XJ56
-
-
-
?
D-Arabinose
D-Ribulose
show the reaction diagram
C0SSE7
-
-
-
?
D-Arabinose
?
show the reaction diagram
-
L-fuculose 1-phosphate is the inducer
-
-
-
D-Arabinose
?
show the reaction diagram
-
the enzyme catalyzes the first reaction in the degradation of D-arabinose
-
-
-
D-Arabinose
?
show the reaction diagram
-
deficiency of the enzyme results in loss of activity to utilize D-arabinose
-
-
-
L-Fucose
?
show the reaction diagram
-
enzyme of the metabolic pathway of L-fucose
-
-
-
L-Fucose
?
show the reaction diagram
-
L-fucose catabolic enzyme
-
-
-
L-Fucose
?
show the reaction diagram
Escherichia coli K12
-
enzyme of the metabolic pathway of L-fucose
-
-
-
L-Fucose
?
show the reaction diagram
Klebsiella pneumoniae W70
-
L-fucose catabolic enzyme
-
-
-
L-galactose
L-tagatose
show the reaction diagram
A4XJ56
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Co2+
-
stimulates
Mn2+
-
stimulates
Mn2+
-
required
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2-amino-2-methyl-1,3-propanediol
-
-
dithioerythritol
-
-
dithiothreitol
-
competitive
EDTA
-
plus L-His
His
-
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
-
-
tert-Butylamine
-
weak
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
98
-
D-arabinose
-
constitutive mutant 531
140
-
D-arabinose
-
wild type strain PRL-R3
160
-
D-arabinose
-
constitutive mutant 502
160
-
D-arabinose
-
D-arabinose
170
-
D-arabinose
-
E. coli B/r
220
-
D-arabinose
-
-
280
-
D-arabinose
-
E. coli K-12
35
-
L-fucose
-
constitutive mutant 531
42
-
L-fucose
-
E. coli B/r
45
-
L-fucose
-
E. coli K-12
50
-
L-fucose
-
constitutive mutant 502
55
-
L-fucose
-
wild type strain PRL-R3
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.1823
-
D-arabinose
A4XJ56
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
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
-
-
after purification, D-galactose as substrate; after purification, D-lyxose as substrate
1.9
-
-
after purification, L-glucose as substrate
2
-
A4XJ56
substrate L-galactose
2.7
-
-
after purification, L-lyxose as substrate
2.8
-
-
after purification, D-mannose as substrate
3
8
-
after purification, L-fucose as substrate
4.7
-
-
after purification, L-xylose as substrate
15
-
A4XJ56
substrate D-altrose
25.1
-
-
D-arabinose, constitutive mutant 502
36.5
-
-
after purification, D-arabinose as substrate
43.5
-
-
L-fucose, constitutuve mutant 502
62
-
A4XJ56
substrate D-arabinose
63.3
-
-
Escherichia coli K-12
63.7
-
-
Escherichia coli B/r
additional information
-
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
9.3
-
-
D-arabinose; L-fucose
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
10
-
7.0: sharp decrease in activity below, 8.0-10.0: maximal activity
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
-
L-fucose induced culture of strain K-12 and D-arabinose-induced culture of strain B/r
Manually annotated by BRENDA team
Escherichia coli B/r
-
L-fucose induced culture of strain K-12 and D-arabinose-induced culture of strain B/r
-
Manually annotated by BRENDA team
Klebsiella pneumoniae M-7
-
-
-
Manually annotated by BRENDA team
Escherichia coli B/r
-
strain K-12
-
Manually annotated by BRENDA team
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
60000
-
-
SDS-PAGE
67000
-
-
SDS-PAGE
68000
-
A4XJ56
determined by SDS-PAGE
68110
-
A4XJ56
theoretical
204000
-
A4XJ56
homotrimer, determined by gel filtration
250000
-
-
gel filtration
342000
-
-
strain B/r, high-speed equilibrium sedimentation
355000
-
-
strain K-12, high-speed equilibrium sedimentation
390000
-
-
-
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hexamer
-
6 * 64976, crystallographic data
hexamer
-
x-ray crystallography
hexamer
Aeribacillus pallidus 14A
-
x-ray crystallography
-
homohexamer
C0SSE7
-
homotrimer
A4XJ56
3 * 68000 Da
tetramer
-
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; 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
tetramer
Escherichia coli B/r
-
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; 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
-
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
sitting drop vapour diffusion method, with 100 mM citrate buffer (final pH 6.0) and 20% (w/v) PEG 3000
-
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
C0SSE7
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
55
-
-
about 40% loss of activity after 10 min without dithiothreitol, stable in presence of dithiothreitol
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
dithiothreitol protects from thermal inactivation at 55 C
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
LITERATURE
Q Sepharose column chromatography, Resource PHE column chromatography, and Resource Q column chromatography
-
using an anion-exchange column, Q Sepharose high performance, a hydrophobic interaction column, RESOURCE PHE, and an anion-exchange column, RESOURCE Q
C0SSE7
on a His-Trap HP column
A4XJ56
of the wild type protein by Q-sepharose HP and Phenyl-sepharose column chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli strain JM109
-
for over-expression in Escherichia coli JM109 cells
C0SSE7
into the vector pGEM-T Easy, and subsequently into the vector pET15b for expression in Escherichia coli ER2566 cells
A4XJ56
nucleotide sequence of the gene fucI
-
organization of the fuc regulon specifying L-fucose dissimilation as determined by gene cloning
-
overexpression in Escherichia coli
-