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Information on EC 4.2.1.90 - L-rhamnonate dehydratase for references in articles please use BRENDA:EC4.2.1.90Word Map on EC 4.2.1.90
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
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L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
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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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C-O bond cleavage by elimination of water
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L-rhamnose degradation II
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L-rhamnose degradation III
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degradation of hexoses
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Fructose and mannose metabolism
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Microbial metabolism in diverse environments
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L-rhamnonate hydro-lyase (2-dehydro-3-deoxy-L-rhamnonate-forming)
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dehydratase, L-rhamnonate
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LRA3
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LraC
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gene name
RhamD
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additional information
the enyzme belongs to the enolase superfamily of enzymes
additional information
the enyzme belongs to the enolase superfamily of enzymes
additional information
the enyzme belongs to the enolase superfamily of enzymes
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gene lraC
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gene lraC
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gene yfaW, strain MG1655
SwissProt
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SwissProt
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SwissProt
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Uniprot
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i.e. Pichia stipitis, gene LRA3
UniProt
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NRC 5568, PR1 mutant
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metabolism
the enzyme is involved in L-rhamnose catabolism. Eukaryotic L-rhamnose pathway, overview
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D-gulonate
? + H2O
low activity
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?
L-lyxonate
2-dehydro-3-deoxy-L-lyxonate + H2O
L-mannonate
2-dehydro-3-deoxy-L-mannonate + H2O
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
additional information
?
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L-lyxonate
2-dehydro-3-deoxy-L-lyxonate + H2O
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?
L-lyxonate
2-dehydro-3-deoxy-L-lyxonate + H2O
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?
L-lyxonate
? + H2O
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?
L-lyxonate
? + H2O
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?
L-lyxonate
? + H2O
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?
L-lyxonate
? + H2O
best substrate, 128% activity compared to L-rhamnonate
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?
L-lyxonate
? + H2O
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best substrate, 128% activity compared to L-rhamnonate
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?
L-mannonate
2-dehydro-3-deoxy-L-mannonate + H2O
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?
L-mannonate
2-dehydro-3-deoxy-L-mannonate + H2O
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?
L-mannonate
?
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?
L-mannonate
? + H2O
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?
L-mannonate
? + H2O
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?
L-mannonate
? + H2O
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?
L-mannonate
? + H2O
89.2% activity compared to L-rhamnonate
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?
L-mannonate
? + H2O
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89.2% activity compared to L-rhamnonate
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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
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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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?
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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?
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
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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
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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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?
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
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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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?
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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L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
L-lyxonate
? + H2O
Q1NEI8
best substrate, 128% activity compared to L-rhamnonate
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?
L-lyxonate
? + H2O
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best substrate, 128% activity compared to L-rhamnonate
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?
L-mannonate
? + H2O
Q1NEI8
89.2% activity compared to L-rhamnonate
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?
L-mannonate
? + H2O
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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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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
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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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?
L-rhamnonate
2-dehydro-3-deoxy-L-rhamnonate + H2O
A3LZU6
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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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?
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
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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Mg2+
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0.115 - 2.99
L-Rhamnonate
additional information
additional information
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1.6
L-lyxonate
pH 7.9, 25°C, wild-type enzyme
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2
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
0.15
L-mannonate
pH 7.9, 25°C, wild-type enzyme
0.115
L-Rhamnonate
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pH 7.0, 30°C
0.15
L-Rhamnonate
pH 7.9, 25°C, wild-type enzyme
0.25
L-Rhamnonate
pH 7.9, 25°C, wild-type enzyme
1.37
L-Rhamnonate
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pH 7.0, 30°C
2.99
L-Rhamnonate
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pH and temperature not specified in the publication
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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0.02
D-gulonate
pH 7.9, 25°C, wild-type enzyme
0.05
L-lyxonate
pH 7.9, 25°C, wild-type enzyme
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2
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
0.2
L-mannonate
pH 7.9, 25°C, wild-type enzyme
0.72
L-Rhamnonate
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pH 7.0, 30°C
3.2
L-Rhamnonate
pH 7.9, 25°C, wild-type enzyme
3.9
L-Rhamnonate
pH 7.9, 25°C, wild-type enzyme
49.3
L-Rhamnonate
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pH 7.0, 30°C
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7
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assay at
7.9
assay at
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25
assay at
30
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assay at
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Azotobacter vinelandii (strain DJ / ATCC BAA-1303);
D0VX14
Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084);
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720);
C1DMY1
Azotobacter vinelandii (strain DJ / ATCC BAA-1303);
C1DMY1
Azotobacter vinelandii (strain DJ / ATCC BAA-1303);
Q8ZNF9
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720);
Q8ZNF9
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720);
Q8ZNF9
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720);
Q8ZNF9
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720);
Q8ZNF9
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720);
Q8ZNF9
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720);
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additional information
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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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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
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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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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-20°C
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NRC 5568, PR1 mutant, partial; strain 1747, partial
NRC 5568, PR1 mutant, partial; strain 1747, partial
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NRC 5568, PR1 mutant, partial; strain 1747, partial
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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
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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
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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Twerdochlib, A.L.; Pedrosa, F.O.; Funayama, S.; Rigo, L.U.
L-Rhamnose metabolism in Pichia stipitis and Debaryomyces polymorphus
Can. J. Microbiol.
40
896-902
1994
Scheffersomyces stipitis, Schwanniomyces polymorphus, Schwanniomyces polymorphus 1747
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Rigo, L.U.; Marechal, L.R.; Vieira, M.M.; Veiga, L.A.
Oxidative pathway for L-rhamnose degradation in Pullularia pullulans
Can. J. Microbiol.
31
817-822
1985
Aureobasidium pullulans
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Watanabe, S.; Saimura, M.; Makino, K.
Eukaryotic and bacterial gene clusters related to an alternative pathway of non-phosphorylated L-rhamnose metabolism
J. Biol. Chem.
283
20372-20382
2008
Azotobacter vinelandii, Azotobacter vinelandii NBRC 102612, Debaryomyces hansenii, Debaryomyces hansenii NBRC0083, Scheffersomyces stipitis
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Rakus, J.F.; Fedorov, A.A.; Fedorov, E.V.; Glasner, M.E.; Hubbard, B.K.; Delli, J.D.; Babbitt, P.C.; Almo, S.C.; Gerlt, J.A.
Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase
Biochemistry
47
9944-9954
2008
Escherichia coli K-12, Escherichia coli K-12 (P77215), Salmonella enterica subsp. enterica serovar Typhimurium (Q8ZNF9), Salmonella enterica subsp. enterica serovar Typhimurium LT2 (Q8ZNF9)
brenda
Watanabe, S.; Makino, K.
Novel modified version of nonphosphorylated sugar metabolism-an alternative L-rhamnose pathway of Sphingomonas sp
FEBS J.
276
1554-1567
2009
Sphingomonas sp. (Q1NEI8), Sphingomonas sp.
brenda
Motter, F.A.; Kuivanen, J.; Keraenen, H.; Hilditch, S.; Penttilae, M.; Richard, P.
Categorisation of sugar acid dehydratases in Aspergillus niger
Fungal Genet. Biol.
64
67-72
2014
Aspergillus niger, Aspergillus niger ATCC 1015
brenda
Koivistoinen, O.M.; Arvas, M.; Headman, J.R.; Andberg, M.; Penttilae, M.; Jeffries, T.W.; Richard, P.
Characterisation of the gene cluster for L-rhamnose catabolism in the yeast Scheffersomyces (Pichia) stipitis
Gene
492
177-185
2012
Scheffersomyces stipitis (A3LZU6)
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