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Literature summary extracted from

  • Watanabe, S.; Makino, K.
    Novel modified version of nonphosphorylated sugar metabolism-an alternative L-rhamnose pathway of Sphingomonas sp (2009), FEBS J., 276, 1554-1567.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.401 expressed in Escherichia coli DH5alpha cells Sphingomonas sp.
4.1.2.53 expressed in a L-rhamnose-defective mutant of Escherichia coli Azotobacter vinelandii
4.1.2.53 expressed in a L-rhamnose-defective mutant of Escherichia coli Scheffersomyces stipitis
4.2.1.90 gene LRA3, functional expression in Escherichia coli Sphingomonas sp.

Protein Variants

EC Number Protein Variants Comment Organism
4.2.1.90 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 Sphingomonas sp.

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.401 0.646
-
 2-dehydro-3-deoxy-L-rhamnonate at pH 8.0 and 25°C Sphingomonas sp.
1.1.1.401 1.27
-
 2-dehydro-3-deoxy-L-lyxonate at pH 8.0 and 25°C Sphingomonas sp.
1.1.1.401 1.9
-
 2-dehydro-3-deoxy-L-mannonate at pH 8.0 and 25°C Sphingomonas sp.
4.2.1.90 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 Sphingomonas sp.

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.1.1.378 26500
-
 x * 26500, SDS-PAGE Sphingomonas sp.
1.1.1.401 25700
-
-
 Sphingomonas sp.
1.1.1.401 30000
-
 x * 30000, SDS-PAGE Sphingomonas sp.

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.378 L-rhamnose + NAD(P)+ Sphingomonas sp. the enzyme is part of an alternative pathway of L-rhamnose metabolism by which L-rhamnose is converted into pyruvate and L-lactaldehyde, through reaction steps analogous to the Entner-Doudoroff pathway L-rhamnono-1,4-lactone + NAD(P)H + H+
-
 ?
1.1.1.378 L-rhamnose + NAD(P)+ Sphingomonas sp. NBRC 101715 the enzyme is part of an alternative pathway of L-rhamnose metabolism by which L-rhamnose is converted into pyruvate and L-lactaldehyde, through reaction steps analogous to the Entner-Doudoroff pathway L-rhamnono-1,4-lactone + NAD(P)H + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-rhamnonate + NAD+ Sphingomonas sp.
-
 2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-rhamnonate + NAD+ Sphingomonas sp. SKA58
-
 2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
 ?
3.1.1.65 L-rhamnono-1,4-lactone + H2O Sphingomonas sp. alternative L-rhamnose pathway L-rhamnonate
-
 ?
3.1.1.65 L-rhamnono-1,4-lactone + H2O Sphingomonas sp. NBRC 101715 alternative L-rhamnose pathway L-rhamnonate
-
 ?
4.1.2.53 2-dehydro-3-deoxy-L-rhamnonate Azotobacter vinelandii
-
 pyruvate + (L)-lactaldehyde
-
 ?
4.1.2.53 2-dehydro-3-deoxy-L-rhamnonate Scheffersomyces stipitis
-
 pyruvate + (L)-lactaldehyde
-
 ?
4.2.1.90 L-lyxonate Sphingomonas sp. best substrate, 128% activity compared to L-rhamnonate ? + H2O
-
 ?
4.2.1.90 L-mannonate Sphingomonas sp. 89.2% activity compared to L-rhamnonate ? + H2O
-
 ?
4.2.1.90 L-rhamnonate Sphingomonas sp. a step in the rhamnose metabolic pathway, overview 2-dehydro-3-deoxy-L-rhamnonate + H2O
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.378 Sphingomonas sp.
-
-
-
1.1.1.378 Sphingomonas sp. NBRC 101715
-
-
-
1.1.1.401 Sphingomonas sp. Q1NEI6
-
-
1.1.1.401 Sphingomonas sp. SKA58 Q1NEI6
-
-
3.1.1.65 Sphingomonas sp.
-
-
-
4.1.2.53 Azotobacter vinelandii
-
-
-
4.1.2.53 Scheffersomyces stipitis
-
-
-
4.2.1.90 Sphingomonas sp. Q1NEI8
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.378
-
 Sphingomonas sp.
1.1.1.401 Ni-NTA column chromatography and Superdex 200 gel filtration Sphingomonas sp.

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
1.1.1.378 0.62
-
 25°C, pH not specified in the publication, cell-free extract, NADP+-dependent activity Sphingomonas sp.
1.1.1.378 31.7
-
 25°C, pH not specified in the publication, purified enzyme, NAD+-dependent activity Sphingomonas sp.
1.1.1.378 39.8
-
 25°C, pH not specified in the publication, purified enzyme, NADP+-dependent activity Sphingomonas sp.

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.378 L-lyxose + NADP+ activity is 75% compared to the activity with L-rhamnose and NADP+ Sphingomonas sp. ?
-
 ?
1.1.1.378 L-lyxose + NADP+ activity is 75% compared to the activity with L-rhamnose and NADP+ Sphingomonas sp. NBRC 101715 ?
-
 ?
1.1.1.378 L-mannose + NADP+ activity is 8.4% compared to the activity with L-rhamnose and NADP+ Sphingomonas sp. ?
-
 ?
1.1.1.378 L-mannose + NADP+ activity is 8.4% compared to the activity with L-rhamnose and NADP+ Sphingomonas sp. NBRC 101715 ?
-
 ?
1.1.1.378 L-rhamnose + NAD(P)+ the enzyme is part of an alternative pathway of L-rhamnose metabolism by which L-rhamnose is converted into pyruvate and L-lactaldehyde, through reaction steps analogous to the Entner-Doudoroff pathway Sphingomonas sp. L-rhamnono-1,4-lactone + NAD(P)H + H+
-
 ?
1.1.1.378 L-rhamnose + NAD(P)+ the enzyme is part of an alternative pathway of L-rhamnose metabolism by which L-rhamnose is converted into pyruvate and L-lactaldehyde, through reaction steps analogous to the Entner-Doudoroff pathway Sphingomonas sp. NBRC 101715 L-rhamnono-1,4-lactone + NAD(P)H + H+
-
 ?
1.1.1.378 L-rhamnose + NAD+
-
 Sphingomonas sp. L-rhamnono-1,4-lactone + NADH + H+
-
 ?
1.1.1.378 L-rhamnose + NAD+
-
 Sphingomonas sp. NBRC 101715 L-rhamnono-1,4-lactone + NADH + H+
-
 ?
1.1.1.378 L-rhamnose + NADP+
-
 Sphingomonas sp. L-rhamnono-1,4-lactone + NADPH + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-lyxonate + NAD+
-
 Sphingomonas sp. 2,4-didehydro-3-deoxy-L-lyxonate + NADH + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-lyxonate + NAD+
-
 Sphingomonas sp. SKA58 2,4-didehydro-3-deoxy-L-lyxonate + NADH + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-mannonate + NAD+
-
 Sphingomonas sp. 2,4-didehydro-3-deoxy-L-mannonate + NADH + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-mannonate + NAD+
-
 Sphingomonas sp. SKA58 2,4-didehydro-3-deoxy-L-mannonate + NADH + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-rhamnonate + NAD+
-
 Sphingomonas sp. 2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
 ?
1.1.1.401 2-dehydro-3-deoxy-L-rhamnonate + NAD+
-
 Sphingomonas sp. SKA58 2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
 ?
3.1.1.65 L-rhamnono-1,4-lactone + H2O alternative L-rhamnose pathway Sphingomonas sp. L-rhamnonate
-
 ?
3.1.1.65 L-rhamnono-1,4-lactone + H2O alternative L-rhamnose pathway Sphingomonas sp. NBRC 101715 L-rhamnonate
-
 ?
4.1.2.53 2-dehydro-3-deoxy-L-rhamnonate
-
 Azotobacter vinelandii pyruvate + (L)-lactaldehyde
-
 ?
4.1.2.53 2-dehydro-3-deoxy-L-rhamnonate
-
 Scheffersomyces stipitis pyruvate + (L)-lactaldehyde
-
 ?
4.2.1.90 L-lyxonate best substrate, 128% activity compared to L-rhamnonate Sphingomonas sp. ? + H2O
-
 ?
4.2.1.90 L-mannonate 89.2% activity compared to L-rhamnonate Sphingomonas sp. ? + H2O
-
 ?
4.2.1.90 L-rhamnonate
-
 Sphingomonas sp. 2-dehydro-3-deoxy-L-rhamnonate + H2O
-
 ?
4.2.1.90 L-rhamnonate a step in the rhamnose metabolic pathway, overview Sphingomonas sp. 2-dehydro-3-deoxy-L-rhamnonate + H2O
-
 ?

Subunits

EC Number Subunits Comment Organism
1.1.1.378 ? x * 26500, SDS-PAGE Sphingomonas sp.
1.1.1.401 ? x * 30000, SDS-PAGE Sphingomonas sp.
1.1.1.401 ? x * 25700, calculated from amino acid sequence Sphingomonas sp.

Synonyms

EC Number Synonyms Comment Organism
1.1.1.378 EAT09360
-
 Sphingomonas sp.
1.1.1.378 LRA1
-
 Sphingomonas sp.
1.1.1.378 NAD(P)+-dependent L-rhamnose-1-dehydrogenase
-
 Sphingomonas sp.
1.1.1.378 SpLRA1
-
 Sphingomonas sp.
1.1.1.401 L-2-keto-3-deoxyrhamnonate-(4)-dehydrogenase
-
 Sphingomonas sp.
1.1.1.401 LKDR 4-dehydrogenase
-
 Sphingomonas sp.
1.1.1.401 LRA5
-
 Sphingomonas sp.
3.1.1.65 L-rhamnono-gamma-lactonase
-
 Sphingomonas sp.
3.1.1.65 LRA2
-
 Sphingomonas sp.
4.1.2.53 L-2-keto-3-deoxyrhamnonate aldolase
-
 Azotobacter vinelandii
4.1.2.53 L-2-keto-3-deoxyrhamnonate aldolase
-
 Scheffersomyces stipitis
4.1.2.53 L-KDR aldolase
-
 Azotobacter vinelandii
4.1.2.53 L-KDR aldolase
-
 Scheffersomyces stipitis
4.1.2.53 LRA4
-
 Azotobacter vinelandii
4.1.2.53 LRA4
-
 Scheffersomyces stipitis
4.2.1.90 LRA3
-
 Sphingomonas sp.

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.401 0.012
-
 2-dehydro-3-deoxy-L-mannonate at pH 8.0 and 25°C Sphingomonas sp.
1.1.1.401 0.18
-
 2-dehydro-3-deoxy-L-lyxonate at pH 8.0 and 25°C Sphingomonas sp.
1.1.1.401 0.86
-
 2-dehydro-3-deoxy-L-rhamnonate at pH 8.0 and 25°C Sphingomonas sp.

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.378 NAD+ dual coenzyme specificity between NAD+ and NADP+ Sphingomonas sp.
1.1.1.378 NADP+ dual coenzyme specificity between NAD+ and NADP+ Sphingomonas sp.
1.1.1.401 NAD+
-
 Sphingomonas sp.

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.1.1.401 0.0063
-
 2-dehydro-3-deoxy-L-mannonate at pH 8.0 and 25°C Sphingomonas sp.
1.1.1.401 0.145
-
 2-dehydro-3-deoxy-L-lyxonate at pH 8.0 and 25°C Sphingomonas sp.
1.1.1.401 1.35
-
 2-dehydro-3-deoxy-L-rhamnonate at pH 8.0 and 25°C Sphingomonas sp.