Information on EC 5.3.1.25 - L-Fucose isomerase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
5.3.1.25
-
RECOMMENDED NAME
GeneOntology No.
L-Fucose isomerase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
L-fucopyranose = L-fuculose
show the reaction diagram
-
-
-
-
L-fucopyranose = L-fuculose
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
-, C0SSE7
-
PATHWAY
KEGG Link
MetaCyc Link
Fructose and mannose metabolism
-
fucose degradation
-
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].
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D-Arabinose (L-Fucose) isomerase
-
-
-
-
D-Arabinose isomerase
-
-
-
-
EC 5.3.1.3
-
-
related
-
Fucose isomerase
-
-
-
-
Isomerase, L-fucose
-
-
-
-
L-Fucose isomerase
C0SSE7
D-arabinose isomerase, bifunctional enzyme
L-Fucose isomerase
A4XJ56
D-arabinose isomerase, bifunctional enzyme
L-fucose ketol-isomerase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
60063-83-4
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
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 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-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
Escherichia coli B/r
-
-
-
-
-
D-Arabinose
D-Ribulose
show the reaction diagram
Klebsiella pneumoniae PRL-R3
-
-
-
-
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
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
A4XJ56
-
-
-
?
L-Fucose
L-Fuculose
show the reaction diagram
-, C0SSE7
-
-
-
?
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
Klebsiella pneumoniae PRL-R3
-
-
-
-
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-Xylose
L-Xylulose
show the reaction diagram
Klebsiella pneumoniae, Klebsiella pneumoniae PRL-R3
-
-
-
-
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-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
L-Fuculose
show the reaction diagram
A4XJ56
-
-
-
?
L-Fucose
L-Fuculose
show the reaction diagram
-, C0SSE7
-
-
-
?
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
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Co2+
-
stimulates
Mn2+
-
stimulates
Mn2+
-
required
Mn2+
-, C0SSE7
-
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
-
-
L-fucitol
-, C0SSE7
-
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
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
1.4
-
A4XJ56
purification step crude extract, substrate L-fucose
10
-
A4XJ56
purification step heat treatment, substrate L-fucose
25.1
-
-
D-arabinose, constitutive mutant 502
43.5
-
-
L-fucose, constitutuve mutant 502
63.3
-
-
Escherichia coli K-12
63.7
-
-
Escherichia coli B/r
76
-
A4XJ56
purification step His-Trap column, substrate L-fucose
additional information
-
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
-
A4XJ56
L-fucose isomerization
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
75
-
A4XJ56
L-fucose isomerization
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 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)
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
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
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
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
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
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
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
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
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
-