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Information on EC 5.3.1.25 - L-fucose isomerase
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5.3.1.25 L-fucose isomeraseIUBMB Comments
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 . The enzyme from Escherichia coli can also convert D-arabinose to D-ribulose . The enzyme from the thermophilic bacterium Caldicellulosiruptor saccharolyticus also converts D-altrose to D-psicose and L-galactose to L-tagatose .
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Word Map
- 5.3.1.25
- l-fuculose
-
isomerization
- d-ribulose
- l-1,2-propanediol
- aerogenes
- d-altrose
-
noninducible
- lactaldehyde
- dihydroxyacetone
-
propanediol
- ribitol
-
irretrievably
- synthesis
- medicine
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
l-fucose isomerase, fucose isomerase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
D-Arabinose (L-Fucose) isomerase
-
-
-
-
D-Arabinose isomerase
-
-
-
-
EC 5.3.1.3
-
-
related
-
Fucose isomerase
-
-
-
-
Isomerase, L-fucose
-
-
-
-
L-Fucose isomerase
L-fucose ketol-isomerase
-
-
-
-
L-Fucose isomerase
D-arabinose isomerase, bifunctional enzyme
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-fucopyranose = L-fuculose
protein environment suggests strongly that the reaction belongs to the ene-diol type
-
L-fucopyranose = L-fuculose
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
isomerization
isomerization
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
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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].
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CAS REGISTRY NUMBER
COMMENTARY
60063-83-4
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-Arabinose
?
-
deficiency of the enzyme results in loss of activity to utilize D-arabinose
-
-
?
D-Arabinose
?
-
the enzyme catalyzes the first reaction in the degradation of D-arabinose
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-Arabinose
?
-
deficiency of the enzyme results in loss of activity to utilize D-arabinose
-
-
?
D-Arabinose
?
-
the enzyme catalyzes the first reaction in the degradation of D-arabinose
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Mn2+
additional information
Mn2+
required for maximum activity (more than 10fold stimulation of activity at 1 mM), the enzyme contains one atom per monomer
additional information
Mg2+ and Ca2+ show no crucial effect on the enzyme activity
additional information
-
Mg2+ and Ca2+ show no crucial effect on the enzyme activity
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
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
10
purification step heat treatment, 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
27
mutant enzyme V131A, 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
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
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
76
purification step His-Trap column, substrate L-fucose
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8 - 10
9.3
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
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
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
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
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
wild type and mutant strains which constitutively synthesize the enzyme
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-
brenda
mutants which are capable of utilizing D-arabinose as a sole source of carbon and energy for growth
-
-
brenda
wild type strain PRL-R3 and two constitutive mutants, 502 and 510
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
L-fucose induced culture of strain K-12 and D-arabinose-induced culture of strain B/r
brenda
-
L-fucose induced culture of strain K-12 and D-arabinose-induced culture of strain B/r
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
fucose-processing enzymes fucose isomerase (FcsI), fuculose kinase (FcsK), and fuculose-1-phosphate aldolase (FcsA) act in a sequential manner to ultimately produce dihydroxyacetone phosphate. Fuculose-1-phosphate appears to act as an inducing molecule for activation of the fucose operon. The Streptococcus pneumoniae fucose-processing pathway has a nonmetabolic role in the interaction of this bacterium with its human host
Show AA Sequence and Transmembrane Helices (3878 entries)
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Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
68000
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
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homohexamer
tetramer
homohexamer
6 * 68363, His6-tagged enzyme, calculated from amino acid sequence
homohexamer
-
6 * 68363, His6-tagged enzyme, calculated from amino acid sequence
-
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
tetramer
-
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
-
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
-
tetramer
-
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
-
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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
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
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
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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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
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
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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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
-
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
using an anion-exchange column, Q Sepharose high performance, a hydrophobic interaction column, RESOURCE PHE, and an anion-exchange column, RESOURCE Q
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
into the vector pGEM-T Easy, and subsequently into the vector pET15b for expression in Escherichia coli ER2566 cells
organization of the fuc regulon specifying L-fucose dissimilation as determined by gene cloning
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
-
the Streptococcus pneumoniae fucose-processing pathway has a nonmetabolic role in the interaction of this bacterium with its human host
synthesis
two-step enzymatic strategy for the synthesis of 6-deoxy-L-sorbose. First, the isomerization of L-fucose to L-fuculose,and the epimerization of L-fuculose to 6-deoxy-L-sorbose catalyzed by D-tagatose 3-epimerase are coupled with the targeted phosphorylation of 6-deoxy-L-sorbose by human fructose kinase in a one-pot reaction. In the second reaction step, the phosphate group of the 6-deoxy-L-sorbose 1-phosphate is hydrolyzed with acid phosphatase to produce 6-deoxy-L-sorbose in 81% yield with regard to L-fucose
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Garcia-Junceda, E.; Shen, G.J.; Alajarin, R.; Wong, C.H.
Cloning and overexpression of rhamnose isomerase and fucose isomerase
Bioorg. Med. Chem.
3
1349-1355
1995
Escherichia coli
brenda
Mortlock, R.P.
D-Arabinose isomerase
Methods Enzymol.
9
583-585
1966
Klebsiella pneumoniae, Klebsiella pneumoniae PRL-R3
-
brenda
Oliver, E.J.; Mortlock, R.P.
Competitive inhibition of an L-fucose isomerase activity by dithiothreitol
Biochem. Biophys. Res. Commun.
36
24-29
1969
Klebsiella pneumoniae
brenda
Oliver, E.J.; Mortlock, R.P.
Metabolism of D-arabinose by Aerobaceter aerogenes: Purification of the isomerase
J. Bacteriol.
108
293-299
1971
Klebsiella pneumoniae
brenda
Oliver, E.J.; Mortlock, R.P.
Growth of Aerobacter aerogenes on D-arabinose: origin of the enzyme activities
J. Bacteriol.
108
287-292
1971
Klebsiella pneumoniae
brenda
Boulter, J.R.; Gielow, W.O.
Properties of D-arabinose isomerase purified from two strains of Escherichia coli
J. Bacteriol.
113
687-696
1973
Escherichia coli, Escherichia coli B/r
brenda
Izumori, K.; Yamanaka, K.
Purification and crystallization of D-arabinose (L-fucose) isomerase from Aerobacter aerogenes by polyethylene glycol
Agric. Biol. Chem.
38
267-273
1974
Klebsiella pneumoniae, Klebsiella pneumoniae M-7
-
brenda
Yamanaka, K.; Izumori, K.
D-Arabinose (L-fucose) isomerase from Aerobacter aerogenes
Methods Enzymol.
41B
462-465
1975
Klebsiella pneumoniae, Klebsiella pneumoniae M-7
brenda
Yamanaka, K.; Izumori, K.
Inhibition of D-arabinose (L-fucose) isomerase activity by Tris and its analogues
Agric. Biol. Chem.
40
439-440
1976
Klebsiella pneumoniae, Klebsiella pneumoniae M-7
-
brenda
Old, D.C.; Mortlock, R.P.
The metabolism of D-arabinose by Salmonella typhimurium
J. Gen. Microbiol.
101
341-344
1977
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Izumori, K.; Yamanaka, K.
Activation and inhibition of D-arabinose isomerase of Klebsiella aerogenes by L-histidine
Agric. Biol. Chem.
43
1993-1994
1979
Klebsiella pneumoniae
-
brenda
Bartkus, J.M.; Mortlock, R.P.
Isolation of a mutation resulting in constitutive synthesis of L-fucose catabolic enzymes
J. Bacteriol.
165
710-714
1986
Escherichia coli
brenda
Seemann, J.E.; Schulz, G.E.
Structure and mechanism of L-fucose isomerase from Escherichia coli
J. Mol. Biol.
273
256-268
1997
Escherichia coli
brenda
LeBlanc D.J.; Mortlock, R.P.
Metabolism of D-arabinose: a new pathway in Escherichia coli
J. Bacteriol.
106
90-96
1971
Escherichia coli
brenda
Lu, Z.; Lin, E.C.C.
The nucleotide sequence of Escherichia coli genes for L-fucose dissimilation
Nucleic Acids Res.
17
4883-4884
1989
Escherichia coli
brenda
Chen, Y.M.; Zhu, Y.; Lin, E.C.C.
The organization of the fuc regulon specifying L-fucose dissimilation in Escherichia coli K12 as determined by gene cloning
Mol. Gen. Genet.
210
331-337
1987
Escherichia coli
brenda
Martin, E.J.St.; Mortlock, R.P.
Natural and altered induction of the L-fuccose catabolic enzymes in Klebsiella aerogenes
J. Bacteriol.
127
91-97
1976
Klebsiella pneumoniae, Klebsiella pneumoniae W70
brenda
Takeda, K.; Yoshida, H.; Izumori, K.; Kamitori, S.
X-ray structures of Bacillus pallidus D-arabinose isomerase and its complex with L-fucitol
Biochim. Biophys. Acta
1804
1359-1368
2010
Aeribacillus pallidus (C0SSE7), Aeribacillus pallidus
brenda
Ju, Y.H.; Oh, D.K.
Characterization of a recombinant L-fucose isomerase from Caldicellulosiruptor saccharolyticus that isomerizes L-fucose, D-arabinose, D-altrose, and L-galactose
Biotechnol. Lett.
32
299-304
2010
Caldicellulosiruptor saccharolyticus (A4XJ56)
brenda
Hong, S.H.; Lim, Y.R.; Kim, Y.S.; Oh, D.K.
Molecular characterization of a thermostable L-fucose isomerase from Dictyoglomus turgidum that isomerizes L-fucose and D-arabinose
Biochimie
94
1926-1934
2012
Dictyoglomus turgidum (B8E1T1), Dictyoglomus turgidum, Dictyoglomus turgidum DSM 6724 (B8E1T1)
brenda
Wen, L.; Huang, K.; Zheng, Y.; Liu, Y.; Zhu, H.; Wang, P.
A two-step strategy for the preparation of 6-deoxy-L-sorbose
Bioorg. Med. Chem. Lett.
26
4358-4361
2016
Escherichia coli (P69922)
brenda
Higgins, M.; Suits, M.; Marsters, C.; Boraston, A.
Structural and functional analysis of fucose-processing enzymes from Streptococcus pneumoniae
J. Mol. Biol.
426
1469-1482
2014
Streptococcus pneumoniae
brenda
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