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Information on EC 1.8.1.5 - 2-oxopropyl-CoM reductase (carboxylating) and Organism(s) Xanthobacter autotrophicus and UniProt Accession Q56839

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IUBMB Comments
Also acts on thioethers longer in chain length on the oxo side, e.g. 2-oxobutyl-CoM, but this portion must be attached to CoM (2-sulfanylethane-1-sulfonate); no CoM analogs will substitute. This enzyme forms component II 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: Q56839
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The taxonomic range for the selected organisms is: Xanthobacter autotrophicus
The enzyme appears in selected viruses and cellular organisms
Synonyms
2-kpcc, nadph:2-ketopropyl-coenzyme m oxidoreductase/carboxylase, 2-ketopropyl-coenzyme m oxidoreductase/carboxylase, 2-ketopropyl coenzyme m oxidoreductase/carboxylase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2-ketopropyl coenzyme M oxidoreductase/carboxylase
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2-ketopropyl-coenzyme M oxidoreductase/carboxylase
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NADPH:2-ketopropyl-coenzyme M carboxylase/oxidoreductase
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NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase
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NADPH:2-ketopropyl-CoM oxidoreductase/carboxylase
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NADPH:2-(2-ketopropylthio)ethanesulfonate oxidoreductase/carboxylase
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NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase
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additional information
enzyme belongs to the disulfide oxidoreductase family of enzymes DSOR
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-mercaptoethanesulfonate + acetoacetate + NADP+ = 2-(2-oxopropylthio)ethanesulfonate + CO2 + NADPH
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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oxidation
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reduction
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
2-mercaptoethanesulfonate,acetoacetate:NADP+ oxidoreductase (decarboxylating)
Also acts on thioethers longer in chain length on the oxo side, e.g. 2-oxobutyl-CoM, but this portion must be attached to CoM (2-sulfanylethane-1-sulfonate); no CoM analogs will substitute. This enzyme forms component II 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
244301-63-1
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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
2-(2-oxopropylthio)ethanesulfonate + CO2 + NADPH
2-mercaptoethanesulfonate + acetoacetate + NADP+
show the reaction diagram
2-(2-oxopropylthio)ethanesulfonate + CO2 + NADPH + H+
2-mercaptoethanesulfonate + acetoacetate + NADP+
show the reaction diagram
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?
2-oxopropyl-coenzyme M + CO2 + NADPH
coenzyme M + acetoacetate + NADP+
show the reaction diagram
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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
2-(2-oxopropylthio)ethanesulfonate + CO2 + NADPH
2-mercaptoethanesulfonate + acetoacetate + NADP+
show the reaction diagram
2-oxopropyl-coenzyme M + CO2 + NADPH
coenzyme M + acetoacetate + NADP+
show the reaction diagram
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
binding domain structure analysis
NADPH
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acetoacetate
mixed noncompetitive inhibition
bromoethanesulfonate
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2-bromoethanesulfonate
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reversible inhibitor, time-dependent inactivator of dithiothreitol-reduced 2-ketopropyl-CoM carboxylase/oxidoreductase, where the redox active cysteines are in the free thiol forms, does not inactivate air-oxidized 2-ketopropyl-CoM carboxylase/oxidoreductase, where the redox active cysteine pair is in the disulfide form. Inactivation leads to covalent modification of the interchange thiol residue C82. The flavin thiol Cys87 is not alkylated by 2-bromoethanesulfonate under reducing conditions, and no amino acid residues are modified by 2-bromoethanesulfonate in the oxidized enzyme
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.42 - 6.37
2-(2-oxopropylthio)ethanesulfonate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.072 - 0.22
2-(2-oxopropylthio)ethanesulfonate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.011 - 0.53
2-(2-oxopropylthio)ethanesulfonate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme belongs to the disulfide oxidoreductase (DSOR) family of enzymes. The characteristic His-Glu catalytic dyad of the DSOR family is replaced in 2-ketopropyl coenzyme M oxidoreductase/carboxylase (2-KPCC) uniquely by the residues Phe-His, potentially to eliminate proton-donating groups at a key position in the active site. These differences in 2-KPCC are key in discriminating between carbon dioxide and protons as attacking electrophiles
physiological function
2-oxopropylcoenzyme M oxidoreductase/carboxylase (2-KPCC) catalyzes the reductive cleavage and carboxylation of 2-oxopropyl coenzyme M (2-KPC) to form acetoacetate and concomitantly regenerate CoM (2-mercaptoethanesulfonate)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
crystal structure
homodimer
x-ray crystallography
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
enzyme free or bound to substrate 2-ketopropyl-CoM, X-ray structure determination and analysis at 1.6-3.5 A resolution, multiple isomorphous replacement and anomalous scattering using four weak heavy atom derivatives
hanging drop vapour diffusion method
in complex with acetoacetate and 2-mercaptoethanesulfonate. In the substrate encapsulated state of the enzyme, CO2 is bound at the base of a narrow hydrophobic substrate access channel. The base of the channel is demarcated by a transition from a hydrophobic to hydrophilic environment where CO2 is located in position for attack on the carbanion of the ketopropyl group of the substrate to ultimately produce acetoacetate. This binding mode effectively discriminates against H2O and prevents protonation of the ketopropyl leaving group
vapor diffusion method, using 0.17 M ammonium acetate, 0.085 M trisodium citrate, pH 5.6, 27% (w/v) PEG 4000, and 15% (v/v) glycerol
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C82A
mutagenesis of the interchange thiol, abolishes all redox-dependent reactions. Redox-independent acetoacetate decarboxylation is not decreased
C87A
mutagenesis of the flavin thiol, results in an inactive enzyme for steady-state redox-dependent reactions, but this variant catalyzes a single-turnover reaction producing a 0.8:1 ratio of product to enzyme. Redox-independent acetoacetate decarboxylation is not decreased
F501H
the mutant shows 10% acetoacetate production activity compared to the wild type enzyme. The overall rate of NADPH turnover remains relatively unchanged in the F501H variant relative to wild type. Moreover, acetone formation by F501H is comparable in rate to the carboxylation reaction catalyzed by wild type enzyme and leading to acetoacetate
F501H/H506E
H137A
mutagenesis of the histidine proximal to the ordered water molecule, leads to nearly complete loss of redox-dependent reactions. Redox-independent acetoacetate decarboxylation is not decreased
H506E
the mutant shows 37% acetoacetate production activity compared to the wild type enzyme. NADPH turnover is around 1.5fold slower in H506E versus wild type enzyme
H84A
mutagenesis of the distal histidine residue, reduces the redox-dependent activities by 58 to 76%. Redox-independent acetoacetate decarboxylation is not decreased
M140A
residue flanking the substrate, catalytic efficiency for 2-(2-oxopropylthio)ethanesulfonate carboxylation is 47fold lower than that for wild-type
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA resin column chromatography, and DEAE-Sepharose column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3)pLysS cells
expressed in Escherichia coli BL21(DE3)pLysS or BL21(DE3) cells
recombinant expression of wild-type and mutant enzymes in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Nocek, B.; Jang, S.B.; Jeong, M.S.; Clark, D.D.; Ensign, S.A.; Peters, J.W.
Structural basis for CO2 fixation by a novel member of the disulfide oxidoreductase family of enzymes, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase
Biochemistry
41
12907-12913
2002
Xanthobacter autotrophicus (Q56839)
Manually annotated by BRENDA team
Pandey, A.S.; Nocek, B.; Clark, D.D.; Ensign, S.A.; Peters, J.W.
Mechanistic implications of the structure of the mixed-disulfide intermediate of the disulfide oxidoreductase, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase
Biochemistry
45
113-120
2006
Xanthobacter autotrophicus (Q56839)
Manually annotated by BRENDA team
Boyd, J.M.; Clark, D.D.; Kofoed, M.A.; Ensign, S.A.
Mechanism of inhibition of aliphatic epoxide carboxylation by the coenzyme M analog 2-bromoethanesulfonate
J. Biol. Chem.
285
25232-25242
2010
Xanthobacter autotrophicus
Manually annotated by BRENDA team
Pandey, A.S.; Mulder, D.W.; Ensign, S.A.; Peters, J.W.
Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M oxidoreductase/carboxylase
FEBS Lett.
585
459-464
2011
Xanthobacter autotrophicus (Q56839)
Manually annotated by BRENDA team
Kofoed, M.A.; Wampler, D.A.; Pandey, A.S.; Peters, J.W.; Ensign, S.A.
Roles of the redox-active disulfide and histidine residues forming a catalytic dyad in reactions catalyzed by 2-ketopropyl coenzyme M oxidoreductase/carboxylase
J. Bacteriol.
193
4904-4913
2011
Xanthobacter autotrophicus (Q56839)
Manually annotated by BRENDA team
Prussia, G.A.; Gauss, G.H.; Mus, F.; Conner, L.; DuBois, J.L.; Peters, J.W.
Substitution of a conserved catalytic dyad into 2-KPCC causes loss of carboxylation activity
FEBS Lett.
590
2991-2996
2016
Xanthobacter autotrophicus (Q56839)
Manually annotated by BRENDA team
Streit, B.R.; Mattice, J.R.; Prussia, G.A.; Peters, J.W.; DuBois, J.L.
The reactive form of a C-S bond-cleaving, CO2-fixing flavoenzyme
J. Biol. Chem.
294
5137-5145
2019
Xanthobacter autotrophicus (Q56839)
Manually annotated by BRENDA team
Prussia, G.A.; Shisler, K.A.; Zadvornyy, O.A.; Streit, B.R.; DuBois, J.L.; Peters, J.W.
The unique Phe-His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S-C bond cleavage
J. Biol. Chem.
297
100961
2021
Xanthobacter autotrophicus (Q56839)
Manually annotated by BRENDA team