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Literature summary extracted from

  • 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 (2019), Biochem. Mol. Biol. Educ., 47, 124-132 .
    View publication on PubMed

Activating Compound

EC Number Activating Compound Comment Organism Structure
1.1.1.268 ethanesulfonate the addition of ethanesulfonate dramatically increases the enentiomeric excess of (S)-2-butanol produced by all forms of recombinant R-HPCDH except the R152A and R196A mutants. The effect of ethanesulfonate and other additives on (S)-butanol production is termed enantioselective modulation, and it is highly selective for sulfonate containing molecules. The interpretation is that the sulfonate of ethanesulfonate interacts with R152 and R196 in the CoM binding pocket alongside 2-butanone, in a way that discourages a si-face hydride addition to produce (R)-2-butanol Xanthobacter autotrophicus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.268 purified recombinant enzyme, X-ray diffraction structure determination and analysis Xanthobacter autotrophicus
1.1.1.269 purified recombinant enzyme, X-ray diffraction structure determination and analysis Xanthobacter autotrophicus

Protein Variants

EC Number Protein Variants Comment Organism
1.1.1.268 additional information comparison of steady-state kinetics and 2-butanol production arte and stereochemistry of wild-type and mutant enzymes, overview Xanthobacter autotrophicus
1.1.1.268 R152A site-directed mutagenesis, the mutant shows altered substrate specificity and interaction with additives compared to wild-type enzyme Xanthobacter autotrophicus
1.1.1.268 R196A site-directed mutagenesis, the mutant shows altered substrate specificity and interaction with additives compared to wild-type enzyme Xanthobacter autotrophicus
1.1.1.268 R203A site-directed mutagenesis, the mutant shows altered substrate specificity and interaction with additives compared to wild-type enzyme Xanthobacter autotrophicus
1.1.1.268 R209A site-directed mutagenesis, the mutant shows altered substrate specificity and interaction with additives compared to wild-type enzyme Xanthobacter autotrophicus

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.1.1.268 (2S)-2-hydroxypropyl-CoM competitive inhibition Xanthobacter autotrophicus
1.1.1.268 2-(2-methyl-2-hydroxypropylthio)-ethanesulfonate M-HPC, competitive inhibition Xanthobacter autotrophicus
1.1.1.268 CoM mixed inhibition Xanthobacter autotrophicus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.268 additional information
-
 additional information steady-state kinetics, comparison of steady-state kinetics with wild-type an d mutant enzymes, overview Xanthobacter autotrophicus
1.1.1.268 0.1
-
 (2S)-2-hydroxypropyl-CoM recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.102
-
 (2R)-2-hydroxypropyl-CoM recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.75
-
 2-(2-hydroxyethylthio)ethanesulfonate recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 1.08
-
 (2R)-2-octanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 2.64
-
 (2R)-2-heptanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 4.6
-
 (2R)-2-hexanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 20
-
 (2R)-2-pentanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 153
-
 (2S)-2-pentanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 315
-
 (2S)-2-butanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 326
-
 (2R)-2-butanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 1726
-
 2-propanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.268 (2R)-2-hydroxypropyl-CoM + NAD+ Xanthobacter autotrophicus
-
 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.268 (2R)-2-hydroxypropyl-CoM + NAD+ Xanthobacter autotrophicus ATCC BAA-1158
-
 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.269 (2S)-2-hydroxypropyl-CoM + NAD+ Xanthobacter autotrophicus
-
 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.269 (2S)-2-hydroxypropyl-CoM + NAD+ Xanthobacter autotrophicus ATCC BAA-1158
-
 2-oxopropyl-CoM + NADH + H+
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.268 Xanthobacter autotrophicus Q56840
-
-
1.1.1.268 Xanthobacter autotrophicus ATCC BAA-1158 Q56840
-
-
1.1.1.269 Xanthobacter autotrophicus Q56841
-
-
1.1.1.269 Xanthobacter autotrophicus ATCC BAA-1158 Q56841
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
1.1.1.268 2-(R)-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+ active site structure modeling and stereochemistry of reaction mechanism, overview Xanthobacter autotrophicus
a
1.1.1.269 (2S)-2-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+ active site structure modeling and stereochemistry of reaction mechanism, overview Xanthobacter autotrophicus
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.268 (2R)-2-butanol + NAD+
-
 Xanthobacter autotrophicus 2-butanone + NADH + H+
-
 r
1.1.1.268 (2R)-2-heptanol + NAD+
-
 Xanthobacter autotrophicus 2-heptanone + NADH + H+
-
 r
1.1.1.268 (2R)-2-hexanol + NAD+
-
 Xanthobacter autotrophicus 2-hexanone + NADH + H+
-
 r
1.1.1.268 (2R)-2-hydroxypropyl-CoM + NAD+
-
 Xanthobacter autotrophicus 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.268 (2R)-2-hydroxypropyl-CoM + NAD+ substrate binding structure, overview Xanthobacter autotrophicus 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.268 (2R)-2-hydroxypropyl-CoM + NAD+
-
 Xanthobacter autotrophicus ATCC BAA-1158 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.268 (2R)-2-hydroxypropyl-CoM + NAD+ substrate binding structure, overview Xanthobacter autotrophicus ATCC BAA-1158 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.268 (2R)-2-octanol + NAD+
-
 Xanthobacter autotrophicus 2-octanone + NADH + H+
-
 r
1.1.1.268 (2R)-2-pentanol + NAD+
-
 Xanthobacter autotrophicus 2-pentanone + NADH + H+
-
 r
1.1.1.268 (2S)-2-butanol + NAD+ very low activity Xanthobacter autotrophicus 2-butanone + NADH + H+
-
 r
1.1.1.268 (2S)-2-hydroxypropyl-CoM + NAD+ competitive inhibitor to the R-enantiomer of substrate, very low activity Xanthobacter autotrophicus 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.268 (2S)-2-hydroxypropyl-CoM + NAD+ competitive inhibitor to the R-enantiomer of substrate, very low activity Xanthobacter autotrophicus ATCC BAA-1158 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.268 (2S)-2-pentanol + NAD+
-
 Xanthobacter autotrophicus 2-pentanone + NADH + H+
-
 r
1.1.1.268 2-(2-hydroxyethylthio)ethanesulfonate + NADH + H+ very low activity Xanthobacter autotrophicus ?
-
 ?
1.1.1.268 2-butanone + NADH + H+ with no additives present, all forms of recombinant R-HPCDH prefer a re-face hydride addition to produce an enantiomeric excess (EE) of (S)-2-butanol, S- and R-2-butanol are comparably good substrates for the reverse reaction. The sulfonate of ethanesulfonate interacts with R152 and R196 in the CoM binding pocket alongside 2-butanone, in a way that discourages a si-face hydride addition to produce (R)-2-butanol Xanthobacter autotrophicus (2R)-2-butanol + NAD+
-
 r
1.1.1.268 2-butanone + NADH + H+ with no additives present, all forms of recombinant R-HPCDH prefer a re-face hydride addition to produce an enantiomeric excess (EE) of (S)-2-butanol, S- and R-2-butanol are comparably good substrates for the reverse reaction. The sulfonate of ethanesulfonate interacts with R152 and R196 in the CoM binding pocket alongside 2-butanone, in a way that discourages a si-face hydride addition to produce (R)-2-butanol Xanthobacter autotrophicus (2S)-2-butanol + NAD+
-
 r
1.1.1.268 2-propanol + NAD+
-
 Xanthobacter autotrophicus 2-propanone + NADH + H+
-
 r
1.1.1.268 2-propanol + NAD+
-
 Xanthobacter autotrophicus ATCC BAA-1158 2-propanone + NADH + H+
-
 r
1.1.1.268 additional information substrate specificity of the stereochemically different isozymes, R- and S-HPCDH (EC 1.1.1.269) are 41% identical to each other, overview. No activity with (S)-2-hexanol, (S)-2-heptanol, and (S)-2-octanol. Stereochemistry of products from reaction with wild-type and mutant enzymes with or without addition of additives, i.e. CH3CH2SO3- Na+, HSCH2CH2SO3- Na+, CH3CH2COO- Na+, CH3COO- Na+, CH3CH2NH3 +Cl-, CH3CH2OH, Na2SO4, and NaCl, overview Xanthobacter autotrophicus ?
-
-
1.1.1.268 additional information substrate specificity of the stereochemically different isozymes, R- and S-HPCDH (EC 1.1.1.269) are 41% identical to each other, overview. No activity with (S)-2-hexanol, (S)-2-heptanol, and (S)-2-octanol. Stereochemistry of products from reaction with wild-type and mutant enzymes with or without addition of additives, i.e. CH3CH2SO3- Na+, HSCH2CH2SO3- Na+, CH3CH2COO- Na+, CH3COO- Na+, CH3CH2NH3 +Cl-, CH3CH2OH, Na2SO4, and NaCl, overview Xanthobacter autotrophicus ATCC BAA-1158 ?
-
-
1.1.1.269 (2S)-2-hydroxypropyl-CoM + NAD+
-
 Xanthobacter autotrophicus 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.269 (2S)-2-hydroxypropyl-CoM + NAD+ substrate binding structure, overview Xanthobacter autotrophicus 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.269 (2S)-2-hydroxypropyl-CoM + NAD+
-
 Xanthobacter autotrophicus ATCC BAA-1158 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.269 (2S)-2-hydroxypropyl-CoM + NAD+ substrate binding structure, overview Xanthobacter autotrophicus ATCC BAA-1158 2-oxopropyl-CoM + NADH + H+
-
 r
1.1.1.269 additional information substrate specificity of the stereochemically different isozymes, R-HPCDH (EC 1.1.1.268) and S-HPCDH are 41% identical to each other, overview Xanthobacter autotrophicus ?
-
-
1.1.1.269 additional information substrate specificity of the stereochemically different isozymes, R-HPCDH (EC 1.1.1.268) and S-HPCDH are 41% identical to each other, overview Xanthobacter autotrophicus ATCC BAA-1158 ?
-
-

Synonyms

EC Number Synonyms Comment Organism
1.1.1.268 (R)-hydroxypropyl-coenzyme M dehydrogenase
-
 Xanthobacter autotrophicus
1.1.1.268 R-HPCDH
-
 Xanthobacter autotrophicus
1.1.1.268 xecD
-
 Xanthobacter autotrophicus
1.1.1.269 (S)-hydroxypropyl-coenzyme M dehydrogenase
-
 Xanthobacter autotrophicus
1.1.1.269 S-HPCDH
-
 Xanthobacter autotrophicus
1.1.1.269 xecE
-
 Xanthobacter autotrophicus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.268 0.044
-
 (2S)-2-hydroxypropyl-CoM recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.29
-
 2-(2-hydroxyethylthio)ethanesulfonate recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.98
-
 (2R)-2-butanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 1.1
-
 (2R)-2-pentanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 1.7
-
 (2R)-2-octanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 1.8
-
 (2R)-2-heptanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 2.2
-
 (2S)-2-butanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 2.7
-
 (2R)-2-hexanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 2.9
-
 2-propanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 2.9
-
 (2S)-2-pentanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 26.8
-
 (2R)-2-hydroxypropyl-CoM recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.268 NAD+
-
 Xanthobacter autotrophicus
1.1.1.268 NADH
-
 Xanthobacter autotrophicus
1.1.1.269 NAD+
-
 Xanthobacter autotrophicus
1.1.1.269 NADH
-
 Xanthobacter autotrophicus

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
1.1.1.268 0.156
-
 (2S)-2-hydroxypropyl-CoM pH and temperature not specified in the publication, versus (2R)-2-hydroxypropyl-CoM Xanthobacter autotrophicus
1.1.1.268 0.406
-
 2-(2-methyl-2-hydroxypropylthio)-ethanesulfonate pH and temperature not specified in the publication, versus (2R)-2-hydroxypropyl-CoM Xanthobacter autotrophicus
1.1.1.268 2.25
-
 CoM pH and temperature not specified in the publication, competitive versus (2R)-2-hydroxypropyl-CoM Xanthobacter autotrophicus
1.1.1.268 3.62
-
 CoM pH and temperature not specified in the publication, uncompetitive Xanthobacter autotrophicus

General Information

EC Number General Information Comment Organism
1.1.1.268 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 Xanthobacter autotrophicus
1.1.1.268 malfunction substitution of R152 or R196 for alanine inhibits ethanesulfonate binding to the extent that its addition does not increase the EE of (S)-2-butanol produced by these mutants Xanthobacter autotrophicus
1.1.1.268 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 Xanthobacter autotrophicus
1.1.1.268 additional information structure-function relationship, active site structure modeling and stereochemistry of reaction mechanism, overview. The C-terminal domains of SDR enzymes are responsible for imparting substrate specificity. Two arginine residues, R152 and R196, play a key role in substrate binding and stereoselectivity of enzyme R-HPCDH. R152 and R196 bind the sulfonate of 2-oxopropyl-CoM (2-KPC) Xanthobacter autotrophicus
1.1.1.269 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 Xanthobacter autotrophicus
1.1.1.269 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 Xanthobacter autotrophicus
1.1.1.269 additional information structure-function relationship, active site structure modeling and stereochemistry of reaction mechanism, overview. The C-terminal domains of SDR enzymes are responsible for imparting substrate specificity Xanthobacter autotrophicus

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.1.1.268 0.0017
-
 2-propanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.003
-
 (2R)-2-butanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.007
-
 (2S)-2-butanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.019
-
 (2S)-2-pentanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.055
-
 (2R)-2-pentanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.39
-
 2-(2-hydroxyethylthio)ethanesulfonate recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.44
-
 (2S)-2-hydroxypropyl-CoM recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.59
-
 (2R)-2-hexanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 0.68
-
 (2R)-2-heptanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 1.57
-
 (2R)-2-octanol recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus
1.1.1.268 262.75
-
 (2R)-2-hydroxypropyl-CoM recombinant enzyme, pH and temperature not specified in the publication Xanthobacter autotrophicus