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Information on EC 1.1.1.401 - 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD+)
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EC Tree
1.1.1.401 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD+)IUBMB Comments
The enzyme, characterized from the bacteria Sphingomonas sp. SKA58 and Sulfobacillus thermosulfidooxidans, is involved in the non-phosphorylative degradation pathway for L-rhamnose. It does not show any detectable activity with NADP+ or with other aldoses.
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Word Map
- 1.1.1.401
- plasminogen
-
phorbol
- 12-o-tetradecanoylphorbol-13-acetate
-
tissue-type
-
tpa-induced
-
thrombolysis
-
reperfusion
-
occlusion
-
13-acetate
-
clot
-
tpa-treated
- malondialdehyde
-
12-o-tetradecanoyl
-
fibrinolysis
-
embolic
-
carcinoembryonic
-
recanalization
-
12-o-tetradecanoylphorbol
- plasmin
-
thrombus
- upa
-
rankin
-
bermudagrass
-
phorbol-13-acetate
-
tpa-mediated
-
cyfra
-
ninds
-
dismutation
-
turfgrasses
- mn-sod
-
sod-like
-
mniii
-
streptokinase
-
copperii
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Reaction Schemes
Synonyms
sulth_3557, kdrdh, 2-keto-3-deoxy-l-rhamnonate dehydrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2-keto-3-deoxy-L-rhamnonate dehydrogenase
KDRDH
L-2-keto-3-deoxyrhamnonate-(4)-dehydrogenase
L-KDR dehydrogenase
LKDR 4-dehydrogenase
LRA5
Sulth 3557 protein
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-dehydro-3-deoxy-L-rhamnonate + NAD+ = 2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
2-dehydro-3-deoxy-L-rhamnonate:NAD+ 4-oxidoreductase
The enzyme, characterized from the bacteria Sphingomonas sp. SKA58 and Sulfobacillus thermosulfidooxidans, is involved in the non-phosphorylative degradation pathway for L-rhamnose. It does not show any detectable activity with NADP+ or with other aldoses.
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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
2,3-butanediol + NAD+
?
the enzyme also shows weak 2,3-butanediol dehydrogenase activity (11.3% compared to 2-dehydro-3-deoxy-L-rhamnonate)
-
-
?
2,3-butanediol + NAD+
?
the enzyme also shows weak 2,3-butanediol dehydrogenase activity (11.3% compared to 2-dehydro-3-deoxy-L-rhamnonate)
-
-
?
2-dehydro-3-deoxy-L-lyxonate + NAD+
2,4-didehydro-3-deoxy-L-lyxonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-lyxonate + NAD+
2,4-didehydro-3-deoxy-L-lyxonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-mannonate + NAD+
2,4-didehydro-3-deoxy-L-mannonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-mannonate + NAD+
2,4-didehydro-3-deoxy-L-mannonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
100% activity
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
100% activity
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
additional information
?
-
-
enzyme shows low activity towards 2,3-butanediol (11% of the activity with 2-dehydro-3-deoxy-L-rhamnonate), and very little activity towards L-rhamnonate, 2-dehydro-3-deoxy-L-mannonate, L-lyxonate and L-mannonate. No substrates are: aldoses such as D-glucose, D-mannose, D-galactose, D-fructose, D-xylose, D-fucose, D-arabinose, D-lyxose, D-ribose, D-fucose, L-fucose, L-xylose, L-arabinose, L-sorbose, polyols such as sorbitol, mannitol, xylitol, amino acids such as L-threonine, L-serine, alcohols such as methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 1,2-propandiol, 1,3-propandiol, aldonates such as D-gluconate, D-galactonate, D-mannonate, D-arabinonate, D-lyxonate, D-xylonate, organic acids such as pyruvate, D-lactate, L-lactate, aldehydes such as D-lactaldehyde, L-lactaldehyde, acetaldehyde, DL-glyceraldehyde, glycolaldehyde
-
-
?
additional information
?
-
enzyme shows low activity towards 2,3-butanediol (11% of the activity with 2-dehydro-3-deoxy-L-rhamnonate), and very little activity towards L-rhamnonate, 2-dehydro-3-deoxy-L-mannonate, L-lyxonate and L-mannonate. No substrates are: aldoses such as D-glucose, D-mannose, D-galactose, D-fructose, D-xylose, D-fucose, D-arabinose, D-lyxose, D-ribose, D-fucose, L-fucose, L-xylose, L-arabinose, L-sorbose, polyols such as sorbitol, mannitol, xylitol, amino acids such as L-threonine, L-serine, alcohols such as methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 1,2-propandiol, 1,3-propandiol, aldonates such as D-gluconate, D-galactonate, D-mannonate, D-arabinonate, D-lyxonate, D-xylonate, organic acids such as pyruvate, D-lactate, L-lactate, aldehydes such as D-lactaldehyde, L-lactaldehyde, acetaldehyde, DL-glyceraldehyde, glycolaldehyde
-
-
?
additional information
?
-
-
the enzyme shows less than 5% activity with L-rhamnonate, 2-dehydro-3-deoxy-L-mannonate, L-lyxonate, and L-mannonate. The enzyme does not show any detectable activity in the presence of NADP+
-
-
?
additional information
?
-
the enzyme shows less than 5% activity with L-rhamnonate, 2-dehydro-3-deoxy-L-mannonate, L-lyxonate, and L-mannonate. The enzyme does not show any detectable activity in the presence of NADP+
-
-
?
additional information
?
-
the enzyme shows less than 5% activity with L-rhamnonate, 2-dehydro-3-deoxy-L-mannonate, L-lyxonate, and L-mannonate. The enzyme does not show any detectable activity in the presence of NADP+
-
-
?
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NATURAL SUBSTRATE
NATURAL 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
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate + NAD+
2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
no detectable activity with NADP+
-
additional information
no detectable activity with NADP+
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
additional information
additional information
-
activity is not significantly affected by the addition of 5 mM metal ions
additional information
activity is not significantly affected by the addition of 5 mM metal ions
additional information
-
the enzyme activity is not significantly affected by the addition of 5 mM Ca2+, Zn2+, Mg2+, Mn2+, Fe2+, Fe3+, and Ni2+
additional information
the enzyme activity is not significantly affected by the addition of 5 mM Ca2+, Zn2+, Mg2+, Mn2+, Fe2+, Fe3+, and Ni2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
EDTA
5 mM, 73% residual activity; 73.7% residual activity at 5 mM EDTA
EGTA
5 mM, 72% residual activity; 72.9% residual activity at 5 mM EGTA
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2
2-dehydro-3-deoxy-L-rhamnonate
at pH 9.5 and 50°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.06
4.06
after 5.1fold purification, at pH 9.0 and 50°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 11.5
little or no activity below pH 7.0, at pH 11.5 the enzme shows 75% of the activity at pH 9.5
8 - 11
the enzyme has no or little activity at pH below 7.0, about 50% activity at pH 8.0, while the enzyme activity at pH 11.0 is about 75% of that obtained at pH 9.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40 - 80
after 20 min incubation, the enzyme is stable at temperatures below 60°C, maintains 53.8% activity at 70°C, and is almost completely inactive at 80°C
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). KDRDH_SULTA
Sulfobacillus thermosulfidooxidans (strain DSM 9293 / VKM B-1269 / AT-1)
331
0
35695
Swiss-Prot
-
A0A2R8BBC1_9RHOB
326
0
34223
TrEMBL
-
D4GPB2_HALVD
Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
344
0
36581
TrEMBL
-
B1FYF8_PARG4
Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M)
251
0
26308
TrEMBL
-
A0A644Y4C1_9ZZZZ
322
0
34692
TrEMBL
other Location (Reliability: 1)
A0A2R8AUM7_9RHOB
245
0
26081
TrEMBL
-
B1FSL1_PARG4
Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M)
250
0
26566
TrEMBL
-
A0A2R8CEJ2_9RHOB
244
0
25666
TrEMBL
-
A0A644ZYI8_9ZZZZ
323
0
35420
TrEMBL
other Location (Reliability: 2)
A0A645DZV0_9ZZZZ
182
1
20266
TrEMBL
other Location (Reliability: 5)
A0A2R8CF39_9RHOB
326
0
34666
TrEMBL
-
A0A6J5JYR8_9BURK
250
0
26522
TrEMBL
-
A0A346B7X8_9BURK
250
0
26527
TrEMBL
-
A0A6J5BF22_9BURK
250
0
26450
TrEMBL
-
E1QSX6_VULDI
Vulcanisaeta distributa (strain DSM 14429 / JCM 11212 / NBRC 100878 / IC-017)
337
0
37234
TrEMBL
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography and Q-Sepharose column chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli DH5alpha cells
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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. (Q1NEI6), Sphingomonas sp. SKA58 (Q1NEI6)
brenda
Bae, J.; Kim, S.M.; Lee, S.B.
Identification and characterization of 2-keto-3-deoxy-L-rhamnonate dehydrogenase belonging to the MDR superfamily from the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans: implications to L-rhamnose metabolism in archaea
Extremophiles
19
469-478
2015
Sulfobacillus thermosulfidooxidans, Sulfobacillus thermosulfidooxidans (P0DOW0), Sulfobacillus thermosulfidooxidans AT-1 (P0DOW0)
brenda
Reinhardt, A.; Johnsen, U.; Schoenheit, P.
L-Rhamnose catabolism in archaea
Mol. Microbiol.
111
1093-1108
2019
Haloferax volcanii (D4GPB2), Haloferax volcanii, Vulcanisaeta distributa (E1QSX6), Vulcanisaeta distributa, Haloferax volcanii ATCC 29605 (D4GPB2)
brenda
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Release 2023.1 (January 2023)