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
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
COMMENTARY
LITERATURE
isomerization
-
-
-
-
isomerization
-
-
isomerization
C0SSE7
-
isomerization
Klebsiella pneumoniae 40bXX
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
D-arabinose degradation I
-
-
D-arabinose degradation II
-
-
degradation of pentoses
-
-
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
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
UNIPROT
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
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
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
COMMENTARY
LITERATURE
Co2+
-
stimulates
Mn2+
-
stimulates
Mn2+
-
required
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-amino-2-methyl-1,3-propanediol
-
-
dithioerythritol
-
-
dithiothreitol
-
competitive
Dulcitol
-
-
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
-
-
L-Arabitol
-
-
L-fucitol
C0SSE7
-
ribitol
-
-
sorbitol
-
-
tert-Butylamine
-
weak
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
98
D-arabinose
-
constitutive mutant 531
140
D-arabinose
-
wild type strain PRL-R3
152
D-arabinose
A4XJ56
-
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
51
L-fucose
-
-
55
L-fucose
-
wild type strain PRL-R3
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0287
D-Altrose
A4XJ56
-
0.1823
D-arabinose
A4XJ56
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
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
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8 - 10
-
-
9.3
-
D-arabinose; L-fucose
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 10
-
7.0: sharp decrease in activity below, 8.0-10.0: maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
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
Klebsiella pneumoniae M-7
-
-
-
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
Escherichia coli B/r
-
strain K-12
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60000
-
SDS-PAGE
674955
67000
-
SDS-PAGE
690278
68000
A4XJ56
determined by SDS-PAGE
702836
68110
A4XJ56
theoretical
702836
204000
A4XJ56
homotrimer, determined by gel filtration
702836
250000
-
gel filtration
2685, 2686
342000
-
strain B/r, high-speed equilibrium sedimentation
2684
355000
-
strain K-12, high-speed equilibrium sedimentation
2684
390000
-
-
2691
SUBUNITS
ORGANISM
UNIPROT
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
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
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
9
-
-
674955
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
55
-
about 40% loss of activity after 10 min without dithiothreitol, stable in presence of dithiothreitol
2680
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
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
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
-