Information on EC 4.2.1.90 - L-rhamnonate dehydratase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
4.2.1.90
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RECOMMENDED NAME
GeneOntology No.
L-rhamnonate dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C-O bond cleavage by elimination of water
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Fructose and mannose metabolism
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L-rhamnose degradation II
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L-rhamnose degradation III
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Microbial metabolism in diverse environments
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degradation of hexoses
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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 hide
99533-47-8
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene lraC
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Manually annotated by BRENDA team
gene lraC
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-
Manually annotated by BRENDA team
strain NBRC 102612
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Manually annotated by BRENDA team
strain NBRC 102612
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Manually annotated by BRENDA team
strain NBRC0083
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Manually annotated by BRENDA team
strain NBRC0083
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-
Manually annotated by BRENDA team
gene yfaW, strain MG1655
SwissProt
Manually annotated by BRENDA team
strain 1747
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Manually annotated by BRENDA team
strain 1747
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-
Manually annotated by BRENDA team
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Uniprot
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
the enzyme is involved in L-rhamnose catabolism. Eukaryotic L-rhamnose pathway, overview
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-gulonate
? + H2O
show the reaction diagram
low activity
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-
?
L-lyxonate
2-dehydro-3-deoxy-L-lyxonate + H2O
show the reaction diagram
L-lyxonate
? + H2O
show the reaction diagram
L-mannonate
2-dehydro-3-deoxy-L-mannonate + H2O
show the reaction diagram
L-mannonate
?
show the reaction diagram
L-mannonate
? + H2O
show the reaction diagram
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
show the reaction diagram
additional information
?
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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
L-lyxonate
? + H2O
show the reaction diagram
Q1NEI8
best substrate, 128% activity compared to L-rhamnonate
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?
L-mannonate
? + H2O
show the reaction diagram
Q1NEI8
89.2% activity compared to L-rhamnonate
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?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
show the reaction diagram
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.6 - 2
L-lyxonate
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0.06 - 0.15
L-mannonate
0.115 - 2.99
L-Rhamnonate
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.02
D-gulonate
Escherichia coli K-12
P77215
pH 7.9, 25C, wild-type enzyme
0.05 - 2
L-lyxonate
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0.1 - 0.2
L-mannonate
0.72 - 49.3
L-Rhamnonate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
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)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
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
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
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
NRC 5568, PR1 mutant, partial; strain 1747, partial
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene LRA3, functional expression in Escherichia coli
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
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H281N
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
H282N
site-directed mutagenesis
H329N
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
H33N
site-directed mutagenesis, inactive mutant
additional information
Show AA Sequence (674 entries)
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