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Enzyme Nomenclature
Information on EC 4.2.1.90 - L-rhamnonate dehydratase
for references in articles please use BRENDA:EC4.2.1.90
Word Map on EC 4.2.1.90
- 4.2.1.90
- stipitis
- vinelandii
-
azotobacter
-
pichia
- l-lactaldehyde
-
dehydrated
-
nonphosphorylated
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promiscuity
- niger
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ladhs
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entner-doudoroff
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
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EC NUMBER 
COMMENTARY 
4.2.1.90
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RECOMMENDED NAME
GeneOntology No.
L-rhamnonate dehydratase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
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-
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L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
reaction mechanism of the RhamD-catalyzed reaction, overview
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
reaction mechanism of the RhamD-catalyzed reaction, overview
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
reaction mechanism of the RhamD-catalyzed reaction, overview
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C-O bond cleavage by elimination of water
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-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
L-rhamnonate hydro-lyase (2-dehydro-3-deoxy-L-rhamnonate-forming)
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CAS REGISTRY NUMBER
COMMENTARY
99533-47-8
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
the enzyme is involved in L-rhamnose catabolism. Eukaryotic L-rhamnose pathway, overview
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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
L-lyxonate
? + H2O
-
-
-
?
L-lyxonate
? + H2O
best substrate, 128% activity compared to L-rhamnonate
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-
?
L-lyxonate
? + H2O
-
best substrate, 128% activity compared to L-rhamnonate
-
-
?
L-mannonate
? + H2O
-
-
-
?
L-mannonate
? + H2O
-
89.2% activity compared to L-rhamnonate
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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enzyme of an oxidative pathway in the degradation of L-rhamnose
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?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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step in the alternative pathway for L-rhamnose metabolism, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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the catalytic mechanism is similar to those of the known acid-sugar dehydratases in this protein family
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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step in the alternative pathway for L-rhamnose metabolism, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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the catalytic mechanism is similar to those of the known acid-sugar dehydratases in this protein family
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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step in the alternative pathway for L-rhamnose metabolism, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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step in the alternative pathway for L-rhamnose metabolism, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
i.e. 6-deoxy-L-mannonate
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
i.e. 6-deoxy-L-mannonate
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
i.e. 6-deoxy-L-mannonate
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
-
step in the alternative pathway for L-rhamnose metabolism, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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-
-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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-
-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
a step in the rhamnose metabolic pathway, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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a step in the rhamnose metabolic pathway, overview
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?
additional information
?
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the recombinant enzyme shows high activity with L-rhamnonate and L-mannonate
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additional information
?
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the recombinant enzyme shows high activity with L-rhamnonate and L-mannonate
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additional information
?
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L-arabonate, D-gluconate, L-fuconate or D-galactonate at 0.002 or 0.02 M are no substrates
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additional information
?
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stereochemical course of the RhamD-catalyzed reaction, overview
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additional information
?
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stereochemical course of the RhamD-catalyzed reaction, overview
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
L-lyxonate
? + H2O
Q1NEI8
best substrate, 128% activity compared to L-rhamnonate
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-
?
L-lyxonate
? + H2O
-
best substrate, 128% activity compared to L-rhamnonate
-
-
?
L-mannonate
? + H2O
-
89.2% activity compared to L-rhamnonate
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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enzyme of an oxidative pathway in the degradation of L-rhamnose
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?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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step in the alternative pathway for L-rhamnose metabolism, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
-
step in the alternative pathway for L-rhamnose metabolism, overview
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-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
-
step in the alternative pathway for L-rhamnose metabolism, overview
-
-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
-
step in the alternative pathway for L-rhamnose metabolism, overview
-
-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
-
step in the alternative pathway for L-rhamnose metabolism, overview
-
-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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-
-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
-
-
-
?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
Q1NEI8
a step in the rhamnose metabolic pathway, overview
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?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
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a step in the rhamnose metabolic pathway, overview
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?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.6
L-lyxonate
pH 7.9, 25°C, wild-type enzyme
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0.06
L-mannonate
pH 7.9, 25°C, wild-type enzyme
0.25
L-Rhamnonate
pH 7.9, 25°C, wild-type enzyme
additional information
additional information
the kcat/Km value with L-rhamnonate is 26.2fold and 59.2fold higher than those with L-lyxonate and L-mannonate, respectively, mainly due to 13.6fold and 30.2fold higher Km values, respectively
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additional information
additional information
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the kcat/Km value with L-rhamnonate is 26.2fold and 59.2fold higher than those with L-lyxonate and L-mannonate, respectively, mainly due to 13.6fold and 30.2fold higher Km values, respectively
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additional information
additional information
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Michaelis-Menten kinetics, overview
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additional information
additional information
Michaelis-Menten kinetics, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.05
L-lyxonate
pH 7.9, 25°C, wild-type enzyme
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0.1
L-mannonate
pH 7.9, 25°C, wild-type enzyme
3.9
L-Rhamnonate
pH 7.9, 25°C, wild-type enzyme
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.9
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
RhamD crystallizes as an octamer, in agreement with the oligomeric structure determined by gel filtration
additional information
RhamD crystallizes as an octamer, in agreement with the oligomeric structure determined by gel filtration
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
octamer
RhamD contains an N-terminal alpha+beta capping domain and a C-terminal (beta/alpha)7beta-barrel, i.e. a modified TIM-barrel, catalytic domain with the active site located at the interface between the two domains
additional information
additional information
RhamD contains an N-terminal alpha+beta capping domain and a C-terminal (beta/alpha)7beta-barrel, i.e. a modified TIM-barrel, catalytic domain with the active site located at the interface between the two domains
additional information
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RhamD contains an N-terminal alpha+beta capping domain and a C-terminal (beta/alpha)7beta-barrel, i.e. a modified TIM-barrel, catalytic domain with the active site located at the interface between the two domains
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme bound to Mg2+, the protein solution contains 42 mg/mL RhamD in 10 mM HEPES, pH 7.5, 150 mM NaCl, 10 mM L-methionine, and 10% glycerol, the precipitant solution contains 1.2 M ammonium sulfate, 100 mM Tris-HCl, pH 8.5, and 0.2 M lithium sulfate, 2 days, X-ray diffraction structure determination and analysis at 2.1 A resolution, RhamD crystallizes as an octamer
enzyme bound to Mg2+ and 3-deoxy-L-rhamnonate, hanging drop method at room temperature, the protein solution for the Mg2+-enzyme complex contains 9.7 mg/mL RhamD in 10 mM HEPES, pH 7.5, containing 150 mM NaCl, 10 mM L-methionine, 5 mM DTT, 10% glycerol, and 5 mM MgCl2, the precipitant solution contains 2.4 M sodium malonate, pH 7.0, and 5 mM MgCl2, for the tertiary complex the protein solution contains 42 mg/mL RhamD in 10 mM in HEPES, pH 7.5, 150 mm NaCl, 10 mM L-methionine, 5 mM DTT, 10% glycerol, 5 mM MgCl2, and 40 mM 3-deoxy-L-rhamnonate, the precipitant solution contains 60% Tacsimate, pH 7.0, and 5 mM MgCl2, 3-4 days, X-ray diffraction structure determination and analysis at 1.8-2.0 A resolution, RhamD crystallizes as an octamer
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
NRC 5568, PR1 mutant, partial; strain 1747, partial
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene lraC, DNA and amino acid sequencedetermination and analysis, expression in Saccharomyces cerevisiae
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gene yfaW, expression of the His6- or His10-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
the genes for L-rhamnose catabolism RHA1, LRA2, LRA3 and LRA4 but not LADH are clustered, genetic organization, phylogenetic analysis, overview. Functional expression of gene LRA3 in Saccharomyces cerevisiae with a strong constitutive promoter. C-terminally his-tagged protein shows no activity and the activity of the N-terminally tagged protein is reduced by about 95%, so the enzyme is expressed without tagand not purified
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H281N
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
H329N
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
additional information
additional information
introduction of genes LRA1-4 or LRA1-3, LRA5 and LAR6 compensats for the L-rhamnose-defective phenotype of an Escherichia coli mutant
additional information
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introduction of genes LRA1-4 or LRA1-3, LRA5 and LAR6 compensats for the L-rhamnose-defective phenotype of an Escherichia coli mutant
additional information
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introduction of genes LRA1-4 or LRA1-3, LRA5 and LAR6 compensats for the L-rhamnose-defective phenotype of an Escherichia coli mutant
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LINKS TO OTHER DATABASES (specific for EC-Number 4.2.1.90)
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