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Information on EC 1.1.1.269 - 2-(S)-hydroxypropyl-CoM dehydrogenase and Organism(s) Xanthobacter autotrophicus and UniProt Accession Q56841

for references in articles please use BRENDA:EC1.1.1.269
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EC Tree
IUBMB Comments
The enzyme is highly specific for (2S)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.268, 2-(R)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (R)-enantiomer. This enzyme forms component IV 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.
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Xanthobacter autotrophicus
UNIPROT: Q56841
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Word Map
The taxonomic range for the selected organisms is: Xanthobacter autotrophicus
The enzyme appears in selected viruses and cellular organisms
Synonyms
s-hpcdh, (s)-hydroxypropyl-coenzyme m dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
(S)-hydroxypropyl-coenzyme M dehydrogenase
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(S)-hydroxypropyl-coenzyme M dehydrogenase
(S)-hydroxypropylthioethanesulfonate dehydrogenase
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2-(2-(S)-hydroxypropylthio)ethanesulfonate dehydrogenase
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S-HPCDH
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2S)-2-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
show the reaction diagram
active site structure modeling and stereochemistry of reaction mechanism, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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-
-
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oxidation
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-
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reduction
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
2-[2-(S)-hydroxypropylthio]ethanesulfonate:NAD+ oxidoreductase
The enzyme is highly specific for (2S)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.268, 2-(R)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (R)-enantiomer. This enzyme forms component IV 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
369364-40-9
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2S)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
show the reaction diagram
(R)-2-butanol + NAD+
2-butanone + NADH + H+
show the reaction diagram
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-
-
r
(S)-2-butanol + NAD+
2-butanone + NADH + H+
show the reaction diagram
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-
-
r
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 + H+
show the reaction diagram
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-
-
r
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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r
2-oxopropyl-CoM + NADH + H+
2-(R)-hydroxypropyl-CoM + NAD+
show the reaction diagram
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r
(R)-2-butanol + NAD+
2-butanone + NADH + H+
show the reaction diagram
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-
-
r
(S)-2-butanol + NAD+
2-butanone + NADH + H+
show the reaction diagram
-
-
-
r
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 + H+
show the reaction diagram
poor substrate. S-HPCDH3 cannot bind hydroxypropyl-CoM with CoM oriented properly in the sulfonate-binding pocket that consists of residues R211 and K214. R-hydroxypropyl-CoM binds to S-HPCDH3 with a 290-fold lower affinity but in an orientation where the hydroxyl and hydrogen on C2 can be more properly aligned with tyrosine 156 and NAD+, such that kcat decreases by 4.5-fold relative to the natural substrate S-hydroxypropyl-CoM
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r
2-(S)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
show the reaction diagram
2-butanone + NADH + H+
(S)-2-butanol + (R)-2-butanol + NAD+
show the reaction diagram
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without additions, 99.2% (S)-enantiomer + 0.8% (R)-enantiomer, in presence of 1 mM ethansulfonate 99.0% (S)-enantiomer + 2% (R)-enantiomer. Mutant K214A, without additions, 91.6% (S)-enantiomer + 8.4% (R)-enantiomer, in presence of 1 mM ethansulfonate 90.9% (S)-enantiomer + 9.1% (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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r
additional information
?
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substrate specificity of the stereochemically different isozymes, R-HPCDH (EC 1.1.1.268) and S-HPCDH are 41% identical to each other, overview
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2S)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
show the reaction diagram
-
-
-
r
2-(S)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
show the reaction diagram
-
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
competitive
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
competitive
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.096
2-(R)-hydroxypropyl-CoM
pH 7.5, 30°C
0.22
2-(S)-hydroxypropyl-CoM
pH 7.5, 30°C
0.068
2-oxopropyl-CoM
pH 7.5, 30°C
68
(R)-2-butanol
wild-type, pH 7.5, 30°C
28
(S)-2-butanol
wild-type, pH 7.5, 30°C
0.97
2-(2-hydroxyethylthio)ethanesulfonate
wild-type, pH 7.5, 30°C
9.1
2-(R)-hydroxypropyl-CoM
wild-type, pH 7.5, 30°C
0.031 - 9.5
2-(S)-hydroxypropyl-CoM
72 - 180
2-butanone
0.27 - 12
2-oxopropyl-CoM
720 - 1400
2-propanol
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
49
2-(R)-hydroxypropyl-CoM
pH 7.5, 30°C
0.12
2-(S)-hydroxypropyl-CoM
pH 7.5, 30°C
29
2-oxopropyl-CoM
pH 7.5, 30°C
1
(R)-2-butanol
wild-type, pH 7.5, 30°C
2.6
(S)-2-butanol
wild-type, pH 7.5, 30°C
3.8
2-(2-hydroxyethylthio)ethanesulfonate
wild-type, pH 7.5, 30°C
5.5
2-(R)-hydroxypropyl-CoM
wild-type, pH 7.5, 30°C
0.013 - 25
2-(S)-hydroxypropyl-CoM
0.039 - 0.072
2-butanone
8.6 - 11
2-oxopropyl-CoM
1.7 - 2
2-propanol
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
500
2-(R)-hydroxypropyl-CoM
pH 7.5, 30°C
0.53
2-(S)-hydroxypropyl-CoM
pH 7.5, 30°C
420
2-oxopropyl-CoM
pH 7.5, 30°C
0.0148
(R)-2-butanol
wild-type, pH 7.5, 30°C
0.0928
(S)-2-butanol
wild-type, pH 7.5, 30°C
0.6
2-(R)-hydroxypropyl-CoM
wild-type, pH 7.5, 30°C
0.0014 - 790
2-(S)-hydroxypropyl-CoM
0.37 - 0.54
2-butanone
0.75 - 39
2-oxopropyl-CoM
1.4 - 2.4
2-propanol
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.29
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
pH 7.5, 30°C
0.29
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
wild-type, pH 7.5, 30°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme belongs to the short-chain dehydrogenases/reductase (SDR) superfamily of enzymes. The C-terminal domains of SDR enzymes are responsible for imparting substrate specificity
metabolism
(R)- and (S)-hydroxypropyl-coenzyme M dehydrogenase (R- and S-HPCDH), are part of a bacterial pathway of short-chain alkene and epoxide metabolism. R- and S-HPCDH act on different substrate enantiomers in a common pathway
metabolism
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 acommon achiral product 2-ketopropyl-CoM
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, X-ray diffraction structure determination and analysis
purified recombinant S-HPCDH free or bound to substrates 2-(S)-hydroxypropyl-CoM and NAD+, sitting drop vapour diffusion method, mixing of equal volumes of 13 mg/ml protein in buffer containing 25% glycerol, with or without 0.05 mM NAD+ and 0.05 mM 2-(S)-hydroxypropyl-CoM, with well solution containing of 0.1 M Bis-Tris, pH 6.5, 0.35 M ammonium acetate and 27% PEG 3350, X-ray diffraction structure determination and analysis at 1.60 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K214A
substantially reduced catalytic efficiencies with the natural substrates in both the oxidative and reductive direction
R211A
substantially reduced catalytic efficiencies with the natural substrates in both the oxidative and reductive direction
S143A
residue acts as H-bond donor to substrate and in charge stabilization of the transition state, large increase in Km value
Y156A
mutation in general acid/base, large increase in Km value
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Krishnakumar, A.M.; Nocek, B.P.; Clark, D.D.; Ensign, S.A.; Peters, J.W.
Structural basis for stereoselectivity in the (R)- and (S)-hydroxypropylthioethanesulfonate dehydrogenases
Biochemistry
45
8831-8840
2006
Xanthobacter autotrophicus
Manually annotated by BRENDA team
Sliwa, D.A.; Krishnakumar, A.M.; Peters, J.W.; Ensign, S.A.
Molecular basis for enantioselectivity in the (R)- and (S)-hydroxypropylthioethanesulfonate dehydrogenases, a unique pair of stereoselective short-chain dehydrogenases/reductases involved in aliphatic epoxide carboxylation
Biochemistry
49
3487-3498
2010
Xanthobacter autotrophicus, Xanthobacter autotrophicus (Q56841)
Manually annotated by BRENDA team
Bakelar, J.W.; Sliwa, D.A.; Johnson, S.J.
Crystal structures of S-HPCDH reveal determinants of stereospecificity for R- and S-hydroxypropyl-coenzyme M dehydrogenases
Arch. Biochem. Biophys.
533
62-68
2013
Xanthobacter autotrophicus (A7IQH5), Xanthobacter autotrophicus
Manually annotated by BRENDA team
Clark, D.D.
Characterization of the recombinant (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases A case study to augment the teaching of enzyme kinetics and stereoselectivity
Biochem. Mol. Biol. Educ.
47
124-132
2019
Xanthobacter autotrophicus (Q56841), Xanthobacter autotrophicus ATCC BAA-1158 (Q56841)
Manually annotated by BRENDA team