Information on EC 5.3.1.25 - L-fucose isomerase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.3.1.25
-
RECOMMENDED NAME
GeneOntology No.
L-fucose isomerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-fucopyranose = L-fuculose
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Fructose and mannose metabolism
-
-
fucose degradation
-
-
Microbial metabolism in diverse environments
-
-
degradation of hexoses
-
-
SYSTEMATIC NAME
IUBMB Comments
L-fucose 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 from Escherichia coli can also convert D-arabinose to D-ribulose [1]. The enzyme from the thermophilic bacterium Caldicellulosiruptor saccharolyticus also converts D-altrose to D-psicose and L-galactose to L-tagatose [4].
CAS REGISTRY NUMBER
COMMENTARY hide
60063-83-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain B/r
-
-
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
-
-
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-ribose
show the reaction diagram
D-Arabinose
D-Ribulose
show the reaction diagram
L-Fucose
?
show the reaction diagram
L-Fucose
L-Fuculose
show the reaction diagram
L-galactose
L-tagatose
show the reaction diagram
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-ribose
show the reaction diagram
L-Fucose
?
show the reaction diagram
L-Fucose
L-Fuculose
show the reaction diagram
L-galactose
L-tagatose
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
about 2fold stimulation of activity at 1 mM
Zn2+
about 3fold stimulation of activity at 1 mM
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-amino-2-methyl-1,3-propanediol
-
-
Cu2+
inhibitory at 1 mM
dithioerythritol
-
-
dithiothreitol
-
competitive
Dulcitol
-
-
Fe2+
inhibitory at 1 mM
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
ribitol
sorbitol
-
-
tert-Butylamine
-
weak
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
98 - 280
D-arabinose
35 - 385
L-fucose
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1985 - 258.3
L-fucose
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.03 - 3.58
L-fucose
717
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.35
mutant enzyme W510A, using L-fucose as substrate, at pH 7.0 and 80°C
0.47
mutant enzyme D373A, using L-fucose as substrate, at pH 7.0 and 80°C
0.67
mutant enzyme Y451A, using L-fucose as substrate, at pH 7.0 and 80°C
0.93
mutant enzyme Q314A, using L-fucose as substrate, at pH 7.0 and 80°C
1.3
mutant enzyme N404A, using L-fucose as substrate, at pH 7.0 and 80°C
1.4
purification step crude extract, substrate L-fucose
2.1
mutant enzyme H539A, using L-fucose as substrate, at pH 7.0 and 80°C
2.4
mutant enzyme M197A, using L-fucose as substrate, at pH 7.0 and 80°C
2.5
mutant enzyme W102A, using L-fucose as substrate, at pH 7.0 and 80°C
2.6
mutant enzyme F452A, using L-fucose as substrate, at pH 7.0 and 80°C
3.4
mutant enzyme R30A, using L-fucose as substrate, at pH 7.0 and 80°C
4.3
mutant enzyme I199A, using L-fucose as substrate, at pH 7.0 and 80°C
6.8
mutant enzyme N538A, using L-fucose as substrate, at pH 7.0 and 80°C
10
purification step heat treatment, substrate L-fucose
25.1
-
D-arabinose, constitutive mutant 502
27
mutant enzyme V131A, using L-fucose as substrate, at pH 7.0 and 80°C
30
mutant enzyme S405A, using L-fucose as substrate, at pH 7.0 and 80°C
33
wild type enzyme, using L-fucose as substrate, at pH 7.0 and 80°C
43.5
-
L-fucose, constitutuve mutant 502
63.3
-
Escherichia coli K-12
63.7
-
Escherichia coli B/r
76
purification step His-Trap column, substrate L-fucose
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 10
9.3
-
D-arabinose; L-fucose
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8.5
about 80% activity at pH 6.5, 100% activity at pH 7.0, about 80% activity at pH 7.5, about 60% activity at pH 8.0, about 50% activity at pH 8.5
7 - 10
-
7.0: sharp decrease in activity below, 8.0-10.0: maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
65 - 90
about 50% activity at 65°C, about 60% activity at 70°C, about 75% activity at 75°C, 100% activity at 80°C, about 75% activity at 85°C, about 60% activity at 90°C
PDB
SCOP
CATH
ORGANISM
UNIPROT
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
64976
-
6 * 64976, crystallographic data
68363
6 * 68363, His6-tagged enzyme, calculated from amino acid sequence
84600
-
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
-
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
-
gel filtration
342000
-
strain B/r, high-speed equilibrium sedimentation
355000
-
strain K-12, high-speed equilibrium sedimentation
390000
-
-
410000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
-
6 * 64976, crystallographic data
homohexamer
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55
-
about 40% loss of activity after 10 min without dithiothreitol, stable in presence of dithiothreitol
80
the enzyme has half-lives of 20, 12, 7, 5, and 2 h at 65, 70,75, 80, and 85°C, respectively
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
heat treatment and His-Trap affinity chromatography
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 ER2566 cells
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
-
organization of the fuc regulon specifying L-fucose dissimilation as determined by gene cloning
-
overexpression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D373A
the mutation results in a substantial increase in Km value
F452A
the mutation results in decreases in kcat, but has little effect on Km value
I199A
the mutation results in a substantial increase in Km value
M197A
the mutation results in a substantial increase in Km value
N404A
the mutation results in decreases in kcat, but has little effect on Km value
N538A
the mutation results in a substantial increase in Km value
Q314A
the mutation results in a substantial increase in Km value
R30A
the mutation results in decreases in kcat, but has little effect on Km value
S405A
the mutation results in a substantial increase in Km value
V131A
the mutation results in a substantial increase in Km value
W102A
the mutation results in decreases in kcat, but has little effect on Km value
W510A
the mutation results in decreases in kcat, but has little effect on Km value
Y451A
the mutation results in a substantial increase in Km value
D349A
-
inactive
-
D373A
-
the mutation results in a substantial increase in Km value
-
M197A
-
the mutation results in a substantial increase in Km value
-
R30A
-
the mutation results in decreases in kcat, but has little effect on Km value
-
W510A
-
the mutation results in decreases in kcat, but has little effect on Km value
-
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