Information on EC 1.1.1.268 - 2-(R)-hydroxypropyl-CoM dehydrogenase

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The expected taxonomic range for this enzyme is: Xanthobacter

EC NUMBER
COMMENTARY hide
1.1.1.268
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RECOMMENDED NAME
GeneOntology No.
2-(R)-hydroxypropyl-CoM dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-(R)-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
show the reaction diagram
highly specific; The enzyme is highly specific for (R)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (S)-enantiomer. This enzyme forms component III of a four-component enzyme system. Comprising EC 4.2.99.19, 2-hydroxypropyl-CoM lyase, component I, EC 1.8.1.5, 2-oxopropyl-CoM reductase, carboxylating, component II, EC 1.1.1.268, 2-(R)-hydroxypropyl-CoM dehydrogenase, component III, and EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, component IV, that is involved in epoxylalkane carboxylation in Xanthobacter sp. strain Py2
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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redox reaction
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reduction
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
propene degradation
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SYSTEMATIC NAME
IUBMB Comments
2-[2-(R)-hydroxypropylthio]ethanesulfonate:NAD+ oxidoreductase
The enzyme is highly specific for (R)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (S)-enantiomer. This enzyme forms component III of a four-component enzyme system {comprising EC 4.4.1.23 (2-hydroxypropyl-CoM lyase; component I), EC 1.8.1.5 [2-oxopropyl-CoM reductase (carboxylating); component II], EC 1.1.1.268 [2-(R)-hydroxypropyl-CoM dehydrogenase; component III] and EC 1.1.1.269 [2-(S)-hydroxypropyl-CoM dehydrogenase; component IV]} that is involved in epoxyalkane carboxylation in Xanthobacter sp. strain Py2.
CAS REGISTRY NUMBER
COMMENTARY hide
244301-33-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain Py2
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Manually annotated by BRENDA team
strain Py2
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
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the bacterium produces R- and S-HPCDH, EC 1.1.1.268 and EC 1.1.1.269, simultaneously to facilitate transformation of R- and S-enantiomers of epoxy-propane to a common achiral product 2-ketopropyl-CoM
additional information
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structural basis for stereospecificity of R-HPCDH, comparison to S-HPCDH, EC 1.1.1.269, overview. Placement of catalytic residues within the active site of each enzyme is nearly identical, structural differences in the surrounding area provide each enzyme with a distinct substrate binding pocket
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(R)-2-butanol + NAD+
2-butanone + NADH + H+
show the reaction diagram
(R)-2-heptanol + NAD+
2-heptanone + NADH + H+
show the reaction diagram
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-
-
-
?
(R)-2-hexanol + NAD+
2-hexanone + NADH + H+
show the reaction diagram
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-
-
-
?
(R)-2-octanol + NAD+
2-octanone + NADH + H+
show the reaction diagram
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-
-
-
?
(R)-2-pentanol + NAD+
2-pentanone + NADH + H+
show the reaction diagram
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-
-
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?
(S)-2-butanol + NAD+
2-butanone + NADH + H+
show the reaction diagram
(S)-2-pentanol + NAD+
2-pentanone + NADH + H+
show the reaction diagram
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-
-
?
2-(2-hydroxyethylthio)ethanesulfonate + NAD+
2-(2-oxoethylthio)ethanesulfonate + NADH
show the reaction diagram
2-(2-hydroxyethylthio)ethanesulfonate + NAD+
2-(formylmethylthio)ethanesulfonate + NADH + H+
show the reaction diagram
achiral mimic of both R-hydroxypropyl-CoM and S-hydroxypropyl-CoM, substrate for both the R- and S-HPCDH enzymes with identical Km values
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r
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH
show the reaction diagram
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
show the reaction diagram
2-(S)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
show the reaction diagram
oxidation of S-hydroxypropyl-CoM with a kcat that is 402 times less than that for R-hydroxypropyl-CoM
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r
2-butanone + NADH + H+
(S)-2-butanol + (R)-2-butanol + NAD+
show the reaction diagram
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without additions, 71.9% (S)-enantiomer + 28% (R)-enantiomer, in presence of 1 mM ethansulfonate 92.7% (S)-enantiomer + 7.3% (R)-enantiomer
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r
2-oxopropyl-CoM + NADH + H+
2-(R)-hydroxypropyl-CoM + NAD+
show the reaction diagram
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r
2-propanol + NAD+
acetone + NADH + H+
show the reaction diagram
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?
2-[(R)-2-hydroxypropylthio]ethanesulfonate + NAD+
2-(2-ketopropylthio)ethanesulfonate + NADH + H+
show the reaction diagram
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the enzyme is highly specific for the R-enantiomer
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r
2-[(S)-2-hydroxypropylthio]ethanesulfonate + NAD+
2-(2-ketopropylthio)ethanesulfonate + NADH + H+
show the reaction diagram
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the enzyme is highly specific for the R-enantiomer
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r
additional information
?
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R-HPCDH1 can bind either enantiomer of hydroxypropyl-CoM with the CoM moiety oriented properly in the sulfonate-binding pocket consisting of R152 and R196. A high-affinity ternary complex of S-HPC, NAD+ forms, but the misalignment of the hydrogen and hydroxyl groups on C2 relative to NAD+ and the tyrosine general base results in a 403-fold lower turnover rate for the S-enantiomer
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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
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH
show the reaction diagram
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
show the reaction diagram
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanesulfonate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
2-(S)-hydroxypropyl-CoM
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2-bromoethanesulfonate
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CoM-analogue, mixed type inhibitor. 32.7% residual activity at 5 mM, reversible inhibition
2-oxopropyl-CoM
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mixed-type inhibitor with respect to 2-(R)-hydroxypropyl-CoM
ethanesulfonate
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mercaptoethanesulfonate
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methanesulfonate
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NADH
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mixed-type inhibitor with respect to 2-(R)-hydroxypropyl-CoM, competitive inhibition with respect to 2-oxopropyl-CoM
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ethanesulfonate
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1 mM, 5.6fold increase in ratio of turnover number to Km-value for 2-butanone as substrate
methanesulfonate
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1 mM, 5.6fold increase in ratio of turnover number to Km-value for 2-butanone as substrate
propanesulfonate
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1 mM, 1.7fold increase in ratio of turnover number to Km-value for 2-butanone as substrate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
220 - 328
(R)-2-butanol
2.64
(R)-2-heptanol
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pH 7.5, 30C
4.6
(R)-2-hexanol
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pH 7.5, 30C
1.08
(R)-2-octanol
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pH 7.5, 30C
20
(R)-2-pentanol
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pH 7.5, 30C
315 - 350
(S)-2-butanol
153
(S)-2-pentanol
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pH 7.5, 30C
0.96
2-(2-hydroxyethylthio)ethanesulfonate
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pH 7.5, 30C
0.092 - 0.44
2-(2-ketopropylthio)ethanesulfonate
0.096 - 0.124
2-(R)-hydroxypropyl-CoM
0.22
2-(S)-hydroxypropyl-CoM
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pH 7.5, 30C
2 - 84
2-butanone
0.068
2-oxopropyl-CoM
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pH 7.5, 30C
1726
2-propanol
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pH 7.5, 30C
0.102
2-[(R)-2-hydroxypropylthio]ethanesulfonate
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pH 7.5, 30C
0.1
2-[(S)-2-hydroxypropylthio]ethanesulfonate
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pH 7.5, 30C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.98 - 1.9
(R)-2-butanol
1.8
(R)-2-heptanol
Xanthobacter autotrophicus
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pH 7.5, 30C
2.7
(R)-2-hexanol
Xanthobacter autotrophicus
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pH 7.5, 30C
1.7
(R)-2-octanol
Xanthobacter autotrophicus
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pH 7.5, 30C
1.1
(R)-2-pentanol
Xanthobacter autotrophicus
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pH 7.5, 30C
2.2 - 9.3
(S)-2-butanol
2.9
(S)-2-pentanol
Xanthobacter autotrophicus
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pH 7.5, 30C
0.29 - 0.55
2-(2-hydroxyethylthio)ethanesulfonate
1.4 - 27.9
2-(2-ketopropylthio)ethanesulfonate
25.8 - 49
2-(R)-hydroxypropyl-CoM
0.12
2-(S)-hydroxypropyl-CoM
Xanthobacter autotrophicus
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pH 7.5, 30C
0.012 - 0.033
2-butanone
24.5 - 29
2-oxopropyl-CoM
2.9
2-propanol
Xanthobacter autotrophicus
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pH 7.5, 30C
26.8
2-[(R)-2-hydroxypropylthio]ethanesulfonate
Xanthobacter autotrophicus
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pH 7.5, 30C
0.044
2-[(S)-2-hydroxypropylthio]ethanesulfonate
Xanthobacter autotrophicus
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pH 7.5, 30C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8.69
(R)-2-butanol
Xanthobacter autotrophicus
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pH 7.5, 30C
2292
26.4
(S)-2-butanol
Xanthobacter autotrophicus
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pH 7.5, 30C
1990
500
2-(R)-hydroxypropyl-CoM
Xanthobacter autotrophicus
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pH 7.5, 30C
5698
0.53
2-(S)-hydroxypropyl-CoM
Xanthobacter autotrophicus
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pH 7.5, 30C
4101
420
2-oxopropyl-CoM
Xanthobacter autotrophicus
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pH 7.5, 30C
3884
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.29 - 0.406
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
0.156
2-(S)-hydroxypropyl-CoM
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competitive inhibition with respect to 2-(R)-hydroxypropyl-CoM
1.2
2-bromoethanesulfonate
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pH 7.4, 30C
26.7
ethanesulfonate
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mixed-type inhibition with respect to 2-(R)-hydroxypropyl-CoM
2.25
mercaptoethanesulfonate
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mixed-type inhibition with respect to 2-(R)-hydroxypropyl-CoM
147.8
methanesulfonate
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mixed-type inhibition with respect to 2-(R)-hydroxypropyl-CoM
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
63900
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
the tetramer is stabilized by the interaction of the terminal carboxylates of each subunit with divalent metal ions
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
the enzyme is cocrystallized in the presence of (S)-hydroxypropyl-coenzyme M, structure refined to 1.8 A resolution
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme
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to homogeneity, recombinant enzyme
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
R152A
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the ratio of turnover number to Km-value for 2-(2-ketopropylthio)ethanesulfonate is 5192fold lower than the ratio for the wild-type enzyme. The ratio of turnover number to Km-value for 2-butanone is 1.3fold higher than the ratio for the wild-type enzyme
R179A
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no detectable activity with 2-(2-ketopropylthio)ethanesulfonate and 2-butanone
R196A
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the ratio of turnover number to Km-value for 2-(2-ketopropylthio)ethanesulfonate is 1000fold lower than the ratio for the wild-type enzyme. The ratio of turnover number to Km-value for 2-butanone is 2.7fold higher than the ratio for the wild-type enzyme
R203A
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the ratio of turnover number to Km-value for 2-(2-ketopropylthio)ethanesulfonate is 4.3fold lower than the ratio for the wild-type enzyme. The ratio of turnover number to Km-value for 2-butanone is 1.6fold lower than the ratio for the wild-type enzyme
R209A
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the ratio of turnover number to Km-value for 2-(2-ketopropylthio)ethanesulfonate is 2.7fold lower than the ratio for the wild-type enzyme. The ratio of turnover number to Km-value for 2-butanone is 1.4fold lower than the ratio for the wild-type enzyme
K159A
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inactive enzyme
S142A
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greatly reduced activity
S142C
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inactive enzyme
Y155E
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inactive enzyme
Y155F
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inactive enzyme
K159A
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inactive enzyme
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S142A
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greatly reduced activity
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S142C
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inactive enzyme
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Y155E
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inactive enzyme
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Y155F
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inactive enzyme
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